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Items: 1 to 20 of 34

1.

An automated method for detecting alternatively spliced protein domains.

Coelho V, Sammeth M.

Bioinformatics. 2018 Jun 1. doi: 10.1093/bioinformatics/bty425. [Epub ahead of print]

PMID:
29868795
2.

Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni.

Boroni M, Sammeth M, Gava SG, Jorge NAN, Macedo AM, Machado CR, Mourão MM, Franco GR.

Sci Rep. 2018 Mar 1;8(1):3877. doi: 10.1038/s41598-018-22093-3.

3.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes.

Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R.

Nat Commun. 2018 Feb 13;9(1):490. doi: 10.1038/s41467-017-02772-x.

4.

Comparative Genomics in Homo sapiens.

Oti M, Sammeth M.

Methods Mol Biol. 2018;1704:451-472. doi: 10.1007/978-1-4939-7463-4_18.

PMID:
29277878
5.

Comparative Genomics in Drosophila.

Oti M, Pane A, Sammeth M.

Methods Mol Biol. 2018;1704:433-450. doi: 10.1007/978-1-4939-7463-4_17.

PMID:
29277877
6.

Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina).

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K.

PLoS Genet. 2016 Dec 5;12(12):e1006491. doi: 10.1371/journal.pgen.1006491. eCollection 2016 Dec.

7.

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.

Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A; GEUVADIS Consortium, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M.

Sci Rep. 2016 Sep 12;6:32406. doi: 10.1038/srep32406.

8.

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J; GTEx Consortium; Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG.

Science. 2015 May 8;348(6235):666-9. doi: 10.1126/science.1261877.

9.

Human genomics. The human transcriptome across tissues and individuals.

Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A; GTEx Consortium, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R.

Science. 2015 May 8;348(6235):660-5. doi: 10.1126/science.aaa0355.

10.

Analysis of alternative splicing events in custom gene datasets by AStalavista.

Foissac S, Sammeth M.

Methods Mol Biol. 2015;1269:379-92. doi: 10.1007/978-1-4939-2291-8_24.

PMID:
25577392
11.

Nova1 is a master regulator of alternative splicing in pancreatic beta cells.

Villate O, Turatsinze JV, Mascali LG, Grieco FA, Nogueira TC, Cunha DA, Nardelli TR, Sammeth M, Salunkhe VA, Esguerra JL, Eliasson L, Marselli L, Marchetti P, Eizirik DL.

Nucleic Acids Res. 2014 Oct;42(18):11818-30. doi: 10.1093/nar/gku861. Epub 2014 Sep 23.

12.

Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina).

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K.

PLoS Genet. 2014 Aug 14;10(8):e1004496. doi: 10.1371/journal.pgen.1004496. eCollection 2014 Aug. Erratum in: PLoS Genet. 2016 Dec 5;12 (12 ):e1006491.

13.

RNA sequencing identifies dysregulation of the human pancreatic islet transcriptome by the saturated fatty acid palmitate.

Cnop M, Abdulkarim B, Bottu G, Cunha DA, Igoillo-Esteve M, Masini M, Turatsinze JV, Griebel T, Villate O, Santin I, Bugliani M, Ladriere L, Marselli L, McCarthy MI, Marchetti P, Sammeth M, Eizirik DL.

Diabetes. 2014 Jun;63(6):1978-93. doi: 10.2337/db13-1383. Epub 2013 Dec 30.

14.

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M; GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T.

Nat Biotechnol. 2013 Nov;31(11):1015-22. doi: 10.1038/nbt.2702. Epub 2013 Sep 15.

PMID:
24037425
15.

Transcriptome and genome sequencing uncovers functional variation in humans.

Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.

Nature. 2013 Sep 26;501(7468):506-11. doi: 10.1038/nature12531. Epub 2013 Sep 15.

16.

The GEM mapper: fast, accurate and versatile alignment by filtration.

Marco-Sola S, Sammeth M, Guigó R, Ribeca P.

Nat Methods. 2012 Dec;9(12):1185-8. doi: 10.1038/nmeth.2221. Epub 2012 Oct 28.

PMID:
23103880
17.

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.

18.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

19.

The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.

Eizirik DL, Sammeth M, Bouckenooghe T, Bottu G, Sisino G, Igoillo-Esteve M, Ortis F, Santin I, Colli ML, Barthson J, Bouwens L, Hughes L, Gregory L, Lunter G, Marselli L, Marchetti P, McCarthy MI, Cnop M.

PLoS Genet. 2012;8(3):e1002552. doi: 10.1371/journal.pgen.1002552. Epub 2012 Mar 8.

20.

Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.

Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PG.

PLoS One. 2012;7(2):e31410. doi: 10.1371/journal.pone.0031410. Epub 2012 Feb 27.

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