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SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.

2018 Development (Cambridge, England)(13)
PMID:  29945865

Matsushima Wayo, Herzog Veronika A, Neumann Tobias, Gapp Katharina, Zuber Johannes, Ameres Stefan L, Miska Eric A

Principles of Systems Biology, No. 29.

2018 Cell systems(5)
PMID:  29792823

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

2018 RNA biology(6)
PMID:  29671387

Jantsch Michael F, Quattrone Alessandro, O'Connell Mary, Helm Mark, Frye Michaela, Macias-Gonzales Manuel, Ohman Marie, Ameres Stefan, Willems Luc, Fuks Francois, Oulas Anastasis, Vanacova Stepanka, Nielsen Henrik, Bousquet-Antonelli Cecile, Motorin Yuri, Roignant Jean-Yves, Balatsos Nikolaos, Dinnyes Andras, Baranov Pavel, Kelly Vincent, Lamm Ayelet, Rechavi Gideon, Pelizzola Mattia, Liepins Janis, Holodnuka Kholodnyuk Irina, Zammit Vanessa, Ayers Duncan, Drablos Finn, Dahl John Arne, Bujnicki Janusz, Jeronimo Carmen, Almeida Raquel, Neagu Monica, Costache Marieta, Bankovic Jasna, Banovic Bojana, Kyselovic Jan, Valor Luis Miguel, Selbert Stefan, Pir Pinar, Demircan Turan, Cowling Victoria, Schäfer Matthias, Rossmanith Walter, Lafontaine Denis, David Alexandre, Carre Clement, Lyko Frank, Schaffrath Raffael, Schwartz Schraga, Verdel Andre, Klungland Arne, Purta Elzbieta, Timotijevic Gordana, Cardona Fernando, Davalos Alberto, Ballana Ester, O Carroll Donal, Ule Jernej, Fray Rupert

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.

2018 Science (New York, N.Y.);360(6390):800, 805, 800-805.
PMID:  29622725

Muhar Matthias, Ebert Anja, Neumann Tobias, Umkehrer Christian, Jude Julian, Wieshofer Corinna, Rescheneder Philipp, Lipp Jesse J, Herzog Veronika A, Reichholf Brian, Cisneros David A, Hoffmann Thomas, Schlapansky Moritz F, Bhat Pooja, von Haeseler Arndt, Köcher Thomas, Obenauf Anna C, Popow Johannes, Ameres Stefan L, Zuber Johannes

Cell-type specific sequencing of microRNAs from complex animal tissues.

2018 Nature methods(4)
PMID:  29481550

Alberti Chiara, Manzenreither Raphael A, Sowemimo Ivica, Burkard Thomas R, Wang Jingkui, Mahofsky Katharina, Ameres Stefan L, Cochella Luisa

Thiol-linked alkylation of RNA to assess expression dynamics.

2017 Nature methods;14(12):1198, 1204, 1198-1204.
PMID:  28945705

Herzog Veronika A, Reichholf Brian, Neumann Tobias, Rescheneder Philipp, Bhat Pooja, Burkard Thomas R, Wlotzka Wiebke, von Haeseler Arndt, Zuber Johannes, Ameres Stefan L

Genetic and mechanistic diversity of piRNA 3'-end formation.

2016 Nature(7630)
PMID:  27851737

Hayashi Rippei, Schnabl Jakob, Handler Dominik, Mohn Fabio, Ameres Stefan L, Brennecke Julius

Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila.

2016 The EMBO journal(22)
PMID:  27729457

Reimão-Pinto Madalena M, Manzenreither Raphael A, Burkard Thomas R, Sledz Pawel, Jinek Martin, Mechtler Karl, Ameres Stefan L

Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila.

2015 Molecular cell(2)
PMID:  26145176

Reimão-Pinto Madalena M, Ignatova Valentina, Burkard Thomas R, Hung Jui-Hung, Manzenreither Raphael A, Sowemimo Ivica, Herzog Veronika A, Reichholf Brian, Fariña-Lopez Sara, Ameres Stefan L

Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor.

2015 Molecular cell(2)
PMID:  26145174

Bortolamiol-Becet Diane, Hu Fuqu, Jee David, Wen Jiayu, Okamura Katsutomo, Lin Ching-Jung, Ameres Stefan L, Lai Eric C

Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions.

2015 Molecular cell(1)
PMID:  26140366

Herzog Veronika A, Ameres Stefan L

Diversifying microRNA sequence and function.

2013 Nature reviews. Molecular cell biology(8)
PMID:  23800994

Ameres Stefan L, Zamore Phillip D

Long-term, efficient inhibition of microRNA function in mice using rAAV vectors.

2012 Nature methods(4)
PMID:  22388288

Xie Jun, Ameres Stefan L, Friedline Randall, Hung Jui-Hung, Zhang Yu, Xie Qing, Zhong Li, Su Qin, He Ran, Li Mengxin, Li Huapeng, Mu Xin, Zhang Hongwei, Broderick Jennifer A, Kim Jason K, Weng Zhiping, Flotte Terence R, Zamore Phillip D, Gao Guangping

The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1.

2011 Current biology : CB(22)
PMID:  22055293

Han Bo W, Hung Jui-Hung, Weng Zhiping, Zamore Phillip D, Ameres Stefan L

MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression.

2011 Molecular therapy : the journal of the American Society of Gene Therapy(3)
PMID:  21179009

Xie Jun, Xie Qing, Zhang Hongwei, Ameres Stefan L, Hung Jui-Hung, Su Qin, He Ran, Mu Xin, Seher Ahmed Seemin, Park Soyeon, Kato Hiroki, Li Chengjian, Mueller Christian, Mello Craig C, Weng Zhiping, Flotte Terence R, Zamore Phillip D, Gao Guangping

Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins.

2011 RNA (New York, N.Y.)(1)
PMID:  21106652

Ameres Stefan L, Hung Jui-Hung, Xu Jia, Weng Zhiping, Zamore Phillip D

Target RNA-directed trimming and tailing of small silencing RNAs.

2010 Science (New York, N.Y.)(5985)
PMID:  20558712

Ameres Stefan L, Horwich Michael D, Hung Jui-Hung, Xu Jia, Ghildiyal Megha, Weng Zhiping, Zamore Phillip D

Riding in silence: a little snowboarding, a lot of small RNAs.

2010 Silence(1)
PMID:  20230614

Ameres Stefan L, Fukunaga Ryuya

The impact of target site accessibility on the design of effective siRNAs.

2008 Nature biotechnology(5)
PMID:  18438400

Tafer Hakim, Ameres Stefan L, Obernosterer Gregor, Gebeshuber Christoph A, Schroeder Renée, Martinez Javier, Hofacker Ivo L

RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition.

2007 Nucleic acids research;35(11):3752, 3763, 3752-63.
PMID:  17517772

Ameres Stefan L, Shcherbakov Dmitry, Nikonova Ekaterina, Piendl Wolfgang, Schroeder Renée, Semrad Katharina

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