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Items: 27

1.

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

Wolf FA, Hamey FK, Plass M, Solana J, Dahlin JS, Göttgens B, Rajewsky N, Simon L, Theis FJ.

Genome Biol. 2019 Mar 19;20(1):59. doi: 10.1186/s13059-019-1663-x.

2.

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

Plass M, Solana J, Wolf FA, Ayoub S, Misios A, Glažar P, Obermayer B, Theis FJ, Kocks C, Rajewsky N.

Science. 2018 May 25;360(6391). pii: eaaq1723. doi: 10.1126/science.aaq1723. Epub 2018 Apr 19.

PMID:
29674432
3.

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

Piwecka M, Glažar P, Hernandez-Miranda LR, Memczak S, Wolf SA, Rybak-Wolf A, Filipchyk A, Klironomos F, Cerda Jara CA, Fenske P, Trimbuch T, Zywitza V, Plass M, Schreyer L, Ayoub S, Kocks C, Kühn R, Rosenmund C, Birchmeier C, Rajewsky N.

Science. 2017 Sep 22;357(6357). pii: eaam8526. doi: 10.1126/science.aam8526. Epub 2017 Aug 10.

PMID:
28798046
4.

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

Plass M, Rasmussen SH, Krogh A.

PLoS Comput Biol. 2017 Apr 14;13(4):e1005460. doi: 10.1371/journal.pcbi.1005460. eCollection 2017 Apr.

5.

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

Macias S, Cordiner RA, Gautier P, Plass M, Cáceres JF.

Mol Cell. 2015 Dec 17;60(6):873-85. doi: 10.1016/j.molcel.2015.11.011. Epub 2015 Dec 10.

6.

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

Hansen HT, Rasmussen SH, Adolph SK, Plass M, Krogh A, Sanford J, Nielsen FC, Christiansen J.

Genome Biol. 2015 Jun 9;16:123. doi: 10.1186/s13059-015-0687-0.

7.

Drosha Regulates Gene Expression Independently of RNA Cleavage Function.

Gromak N, Dienstbier M, Macias S, Plass M, Eyras E, Cáceres JF, Proudfoot NJ.

Cell Rep. 2014 Jun 12;7(5):1753-1754. doi: 10.1016/j.celrep.2014.05.047. Epub 2014 Jun 12. No abstract available.

8.

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

Rehfeld A, Plass M, Døssing K, Knigge U, Kjær A, Krogh A, Friis-Hansen L.

Front Endocrinol (Lausanne). 2014 Apr 15;5:46. doi: 10.3389/fendo.2014.00046. eCollection 2014.

9.

Approaches to link RNA secondary structures with splicing regulation.

Plass M, Eyras E.

Methods Mol Biol. 2014;1126:341-56. doi: 10.1007/978-1-62703-980-2_25.

PMID:
24549676
10.

Drosha regulates gene expression independently of RNA cleavage function.

Gromak N, Dienstbier M, Macias S, Plass M, Eyras E, Cáceres JF, Proudfoot NJ.

Cell Rep. 2013 Dec 26;5(6):1499-510. doi: 10.1016/j.celrep.2013.11.032. Epub 2013 Dec 19. Erratum in: Cell Rep. 2014 Jun 12;7(5):1753-4.

11.

The Microprocessor controls the activity of mammalian retrotransposons.

Heras SR, Macias S, Plass M, Fernandez N, Cano D, Eyras E, Garcia-Perez JL, Cáceres JF.

Nat Struct Mol Biol. 2013 Oct;20(10):1173-81. doi: 10.1038/nsmb.2658. Epub 2013 Sep 1.

12.

On the accuracy of short read mapping.

Menzel P, Frellsen J, Plass M, Rasmussen SH, Krogh A.

Methods Mol Biol. 2013;1038:39-59. doi: 10.1007/978-1-62703-514-9_3.

PMID:
23872968
13.

Alterations in polyadenylation and its implications for endocrine disease.

Rehfeld A, Plass M, Krogh A, Friis-Hansen L.

Front Endocrinol (Lausanne). 2013 May 8;4:53. doi: 10.3389/fendo.2013.00053. eCollection 2013.

14.

Prophylactic perioperative sodium bicarbonate to prevent acute kidney injury following open heart surgery: a multicenter double-blinded randomized controlled trial.

Haase M, Haase-Fielitz A, Plass M, Kuppe H, Hetzer R, Hannon C, Murray PT, Bailey MJ, Bellomo R, Bagshaw SM.

PLoS Med. 2013;10(4):e1001426. doi: 10.1371/journal.pmed.1001426. Epub 2013 Apr 16.

15.

Low preoperative hepcidin concentration as a risk factor for mortality after cardiac surgery: a pilot study.

Haase-Fielitz A, Plaß M, Kuppe H, Hetzer R, Ostland V, Westphal S, Hoffmann J, Prowle J, Mertens PR, Westerman M, Bellomo R, Haase M.

J Thorac Cardiovasc Surg. 2013 May;145(5):1380-6. doi: 10.1016/j.jtcvs.2012.09.003. Epub 2012 Oct 9.

16.

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor.

Macias S, Plass M, Stajuda A, Michlewski G, Eyras E, Cáceres JF.

Nat Struct Mol Biol. 2012 Aug;19(8):760-6. doi: 10.1038/nsmb.2344. Epub 2012 Jul 15.

17.

RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae.

Plass M, Codony-Servat C, Ferreira PG, Vilardell J, Eyras E.

RNA. 2012 Jun;18(6):1103-15. doi: 10.1261/rna.030767.111. Epub 2012 Apr 26.

18.

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

Meyer M, Plass M, Pérez-Valle J, Eyras E, Vilardell J.

Mol Cell. 2011 Sep 16;43(6):1033-9. doi: 10.1016/j.molcel.2011.07.030.

19.

Urine hepcidin has additive value in ruling out cardiopulmonary bypass-associated acute kidney injury: an observational cohort study.

Haase-Fielitz A, Mertens PR, Plass M, Kuppe H, Hetzer R, Westerman M, Ostland V, Prowle JR, Bellomo R, Haase M.

Crit Care. 2011 Aug 4;15(4):R186. doi: 10.1186/cc10339.

20.

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

Alló M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B, Kornblihtt AR.

Nat Struct Mol Biol. 2009 Jul;16(7):717-24. doi: 10.1038/nsmb.1620. Epub 2009 Jun 21.

PMID:
19543290
21.

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

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ.

Science. 2009 Apr 24;324(5926):522-8. doi: 10.1126/science.1169588.

22.

ASTD: The Alternative Splicing and Transcript Diversity database.

Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D.

Genomics. 2009 Mar;93(3):213-20. doi: 10.1016/j.ygeno.2008.11.003. Epub 2008 Dec 24.

23.

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

Plass M, Agirre E, Reyes D, Camara F, Eyras E.

Trends Genet. 2008 Dec;24(12):590-4. doi: 10.1016/j.tig.2008.10.004. Epub 2008 Nov 5.

PMID:
18992956
24.
25.

Molecular interactions in 3-carboxy-2-diphenylphosphinoylcyclopentanone.

Kolbe A, Plass M, Zurawiński R, Kiełbasiński P, Mikołajczyk M.

Spectrochim Acta A Mol Biomol Spectrosc. 2003 Oct;59(12):2875-81.

PMID:
14499847
26.
27.

isoCitric dehydrogenase and glutamic acid synthesis in animal tissues.

Adler E, Euler HV, Günther G, Plass M.

Biochem J. 1939 Jun;33(6):1028-45. No abstract available.

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