Publications by authors named "Mireya Plass"

21Publications

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.

Genome Biol 2019 03 19;20(1):59. Epub 2019 Mar 19.

Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany.

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http://dx.doi.org/10.1186/s13059-019-1663-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425583PMC
March 2019

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.

Science 2018 05 19;360(6391). Epub 2018 Apr 19.

Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

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http://dx.doi.org/10.1126/science.aaq1723DOI Listing
May 2018

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function.

Science 2017 09 10;357(6357). Epub 2017 Aug 10.

Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, Berlin-Buch, Germany.

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http://dx.doi.org/10.1126/science.aam8526DOI Listing
September 2017

Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.

PLoS Comput Biol 2017 04 14;13(4):e1005460. Epub 2017 Apr 14.

Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1005460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409497PMC
April 2017

DGCR8 Acts as an Adaptor for the Exosome Complex to Degrade Double-Stranded Structured RNAs.

Mol Cell 2015 Dec 10;60(6):873-85. Epub 2015 Dec 10.

Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.11.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691244PMC
December 2015

Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.

Genome Biol 2015 Jun 9;16:123. Epub 2015 Jun 9.

Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/s13059-015-0687-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477473PMC
June 2015

Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors.

Front Endocrinol (Lausanne) 2014 15;5:46. Epub 2014 Apr 15.

Center for Genomic Medicine, Rigshospitalet, University of Copenhagen , Copenhagen , Denmark.

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http://dx.doi.org/10.3389/fendo.2014.00046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995063PMC
April 2014

Approaches to link RNA secondary structures with splicing regulation.

Methods Mol Biol 2014 ;1126:341-56

Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-980-2_25DOI Listing
October 2014

Drosha regulates gene expression independently of RNA cleavage function.

Cell Rep 2013 Dec 19;5(6):1499-510. Epub 2013 Dec 19.

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2013.11.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898267PMC
December 2013

The Microprocessor controls the activity of mammalian retrotransposons.

Nat Struct Mol Biol 2013 Oct 1;20(10):1173-81. Epub 2013 Sep 1.

1] Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK. [2] Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government (GENYO), Granada, Spain. [3].

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http://dx.doi.org/10.1038/nsmb.2658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836241PMC
October 2013

On the accuracy of short read mapping.

Methods Mol Biol 2013 ;1038:39-59

Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-514-9_3DOI Listing
February 2014

Alterations in polyadenylation and its implications for endocrine disease.

Front Endocrinol (Lausanne) 2013 8;4:53. Epub 2013 May 8.

Genomic Medicine, Rigshospitalet, Copenhagen University Hospital Copenhagen, Denmark.

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http://dx.doi.org/10.3389/fendo.2013.00053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3647115PMC
May 2013

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor.

Nat Struct Mol Biol 2012 Aug 15;19(8):760-6. Epub 2012 Jul 15.

Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.

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http://dx.doi.org/10.1038/nsmb.2344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3442229PMC
August 2012

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing.

Mol Cell 2011 Sep;43(6):1033-9

Centre de Regulació Genòmica, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1016/j.molcel.2011.07.030DOI Listing
September 2011

Control of alternative splicing through siRNA-mediated transcriptional gene silencing.

Nat Struct Mol Biol 2009 Jul 21;16(7):717-24. Epub 2009 Jun 21.

Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.

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http://dx.doi.org/10.1038/nsmb.1620DOI Listing
July 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Co-evolution of the branch site and SR proteins in eukaryotes.

Trends Genet 2008 Dec 5;24(12):590-4. Epub 2008 Nov 5.

Computational Genomics Group, Universitat Pompeu Fabra, PRBB, Dr. Aiguader 88 E08003, Barcelona, Spain.

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http://www.cell.com/cms/attachment/592328/4567045/mmc1.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S016895250800271
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http://dx.doi.org/10.1016/j.tig.2008.10.004DOI Listing
December 2008

Differentiated evolutionary rates in alternative exons and the implications for splicing regulation.

BMC Evol Biol 2006 Jun 22;6:50. Epub 2006 Jun 22.

Research Unit of Biomedical Informatics, IMIM - Pompeu Fabra University, E08003, Barcelona, Spain.

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http://dx.doi.org/10.1186/1471-2148-6-50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1543662PMC
June 2006