Publications



DOPAMINET list of scientific publications
N.TitleOther Authors involvedPeriodical or SeriesPlaceDateDoiPermanent IdentifiersOpen Access?URL
1Coding and non-coding transcription initiation landscape at single nucleotide resolsution during vertebrate embryo developmentChirag Nepal, Yavor Hadzhiev, Christopher Previti, Nan Li, Vanja Haberle, Hazuki Takahashi, Ana Maria Suzuki, Ying Sheng, Rehab F. Abdelhamid, Santosh Anand, Jochen Gehrig, Altuna Akalin, Christel E.M. Kockx, Antoine A.J. van der Sloot, Wilfred F.J. van IJcken, Olivier Armant, Sepand Rastegar, Uwe Strähle, Elia Stupka, Piero Carninci, Boris Lenhard and Ferenc Müller(IN PREPARATION)



2Suppression of barcode bias in high-throughput transcriptome analyses utilizing template switchingDave Tang, Charles Plessy, Md Salimullah, Ana Maria Suzuki, Raffaella Calligaris, Stefano Gustincich, Piero Carninci(SUBMITTED)



3UCH-L1 protein synthesis upon rapamycin treatment involves its antisense RNA through embedded SINEB2 repeatsClaudia Carrieri, Marta Biagioli, Laura Cimatti, Anne Beugnet, Isidre Ferrer, Silvia Zucchelli, Stefano Biffo, Sofia Francia, Allistar Forrest, Piero Carninci, Elia Stupka, and Stefano Gustincich(SUBMITTED)



4Site-specific DICER and DROSHA RNA products control the DNA-damage responseFlavia Michelini, Alka Saxena, Dave Tang, Michiel de Hoon, Viviana Anelli, Marina Mione, Piero Carninci & Fabrizio d’Adda di Fagagna
Nature
(2012)
UK23/05/201210.1038/nature11179
YESLink
5Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.Alka Saxena, Akiko Wagatsuma, Yukihiko Noro, Takenobu Kuji, Atsuko Asaka-Oba, Akira Watahiki, Cecile Gurnot, Michela Fagiolini, Takao K. Hensch, and Piero CarninciBioTechniques, Vol. 52, No. 6, June 2012, pp. 381–385USA01//06/2012
PMID:22668417YESLink
6Metazoan promoters: emerging characteristics and insights into transcriptional regulation.Boris, Lenhard Albin Sandelin, Piero CarninciNature Reviews Genetics 13, 233-245 (April 2012)UK06/03/201210.1038/nrg3163PMID:22392219YESLink
7Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs.Alka Saxena, Piero CarninciBioEssays, Vol. 33, Issue 11, pages 830–839, Nov 2011USA01/11/201110.1002/bies.201100084.PMID:21915889YESLink
8Whole transcriptome analysis : What are we still missing?Alka Saxena, Piero CarninciWiley Interdiscip Rev: Syst Biol Med., Vol. 3, Issue 5, pages 527–543, Sep/Oct 2011
USA30/09/201110.1002/wsbm.135PMID:21197667YESLink
9Non-Coding RNA: an OverviewAlka Saxena, Piero CarninciEpigenetics: A Reference Manual, Chapter 16, pages 271-289
UK2011

NO
10NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.Md Salimullah, Sakai Mizuho, Charles Plessy, Piero CarninciCold Spring Harb Protoc 2011
USA01/01/201110.1101/pdb.prot5559PMID:21205859YESLink
11Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md. Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A. Davis, Thomas R. Gingeras, Jun Kawai, Carsten O. Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero CarninciNature Methods 7, 528–534 (July 2010)USA13/06/201010.1038/nmeth.1470PMID:20543846YESLink
12Tunable fractionation of nucleic acids.Md Salimullah, Sachiko Kato, Mitsuyoshi Murata, Chika Kawazu, Charles Plessy, Piero CarninciBioTechniques, Vol. 47, No. 6, December 2009, pp. 1041–1043USA06/12/200910.2144/000113249PMID:20041857YESLink
13RNA dust: where are the genes?Piero CarninciDNA Research, (2010) 17 (2): 51-59
UK07/03/201010.1093/dnares/dsq006PMID:20211845YESLink
14RNA dust: where are the genes? (Japanese Translation)Yukihiko Noro, Piero CarninciExperimental Medicine, Vol. 28, pages 190-195
Japan01/09/2010

NO
15Automated feature detection and imaging for high-resolution screening of zebrafish embryos.Ravindra Peravali, Jochen Gehrig, Stefan Giselbrecht, Dominic S Lütjohann, Yavor Hadzhiev, Ferenc Müller and Urban LiebelBiotechniques 50(5):319-24 (2011)USA01/05/2011
PMID 21548893YESLink
16"Sciencenet" - Towards a global search and share engine for all scientific knowledgeD S Lutjohann, A H Shah, M P Christen, F Richter, K Knese and U LiebelBioinformaticsUSA15/06/2011
PMID 21493657YESLink
17Comprehensive catecholaminergic projectome analysis reveals single neuron integration of zebrafish ascending and descending dopaminergic systems.Tuan Leng Tay, Olaf Ronneberger, Soojin Ryu, Roland Nitschke, and Wolfgang DrieverNature CommunicationsUK25/01/201110.1038/ncomms1171


18ParkDB: a Parkinson’s disease gene expression databaseCristian Taccioli, Vincenza Maselli, Jesper Tegnér, David Gomez-Cabrero, Gioia Altobelli, Warren Emmett4, Francesco Lescai, Stefano Gustincich and Elia StupkaDatabase the Journal of Biological Databasess and Curation (2011)
UK09/03/201110.1093/database/bar007
YESLink
19Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome ActivationL. C. Lindeman, I.S. Andersen, A.H. Reiner, N. Li, Håvard, Aanes, O. Østrup, C. Winata, S. Mathavan, F. Müller, P. Aleström, and P. CollasDevelopmental Cell, Vol. 21, Issue 6, 993-1004, Dec 2011CH13/12/201110.1016/j.devcel.2011.10.008

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20Novel SPG11 mutations in Asian kindreds and disruption of spatacsin function in the zebrafishSouthgate, L, Dafou D., Hoyle J, Li N, Kinning E, Critchley P, Németh AH, Talbot K, Bindu PS, Sinha S, Taly AB, Raghavendra S, Müller F, Maher ER, Trembath RC.Neurogenetics: 11(4) Oct 2010, pages 379-389
01/10/2010
PMID:20390432

21Developmental regulation of transcription initiation: more than just changing the actorsMüller F., Zaucker A., Tora L.Curr Opin Genes Dev., 20(5) Oct 2010 ,pages 533-540NL01/10/2010
PMID: 20598874

22Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryosGehrig J, Reischl M, Kalmár E, Ferg M, Hadzhiev Y, Zaucker A, Song C, Schindler S, Liebel U. and Müller F.Nature Methods: 6(12) Nov 2009, pages 911-916
UK08/11/200910.1038/nmeth.1396


23Parkinson's disease DJ-1 L166P alters rRNA biogenesis by exclusion of TTRAP from the nucleolus and sequestration into cytoplasmic aggregates via TRAF6Vilotti S, Codrich M, Dal Ferro M, Pinto M, Ferrer I, Collavin L, Gustincich S, Zucchelli S.PLoS One. 2012;7(4):e35051. Epub 2012 Apr 20.USA20/04/2012epub22532838
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24Direct generation of functional dopaminergic neurons from mouse and human fibroblasts.Caiazzo M, Dell'Anno MT, Dvoretskova E, Lazarevic D, Taverna S, Leo D, Sotnikova TD, Menegon A, Roncaglia P, Colciago G, Russo G, Carninci P, Pezzoli G, Gainetdinov RR, Gustincich S, Dityatev A, Broccoli VNature. 2011 Jul 3;476(7359):224-7UK03/07/201110.1038/nature1028421725324
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25Brain development, plasticity and ageing in health and disease -Consensus Document on European Brain ResearchC. Arango, S. Gustincich, O. Marin, J. Parnavelas, M. SmidtEuropean Journal of Neuroscience: Vol. 33, 3 Jul 2011, pages 770–772
USA03/07/201110.1111/j.1460-9568.2010.7596.x


26Promoter architecture of mouse olfactory receptor genes.Plessy C, Pascarella G, Bertin N, Akalin A, Carrieri C, Vassalli A, Lazarevic D, Severin J, Vlachouli C, Simone R, Faulkner GJ, Kawai J, Daub CO, Zucchelli S, Hayashizaki Y, Mombaerts P, Lenhard B, Gustincich S, Carninci P.Genome Res. 2012 March; 22(3): 486–497USA22/12/2011
22194471
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