Publications

Papers co-authored by the Lab

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. Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina). PLoS Genet. 2016;12 (12):e1006491. doi: 10.1371/journal.pgen.1006491. PubMed PMID:27918580 PubMed Central PMC5137873.

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. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Sci Rep. 2016;6 :32406. doi: 10.1038/srep32406. PubMed PMID:27617755 PubMed Central PMC5019111.

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. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 2015;348 (6235):666-9. doi: 10.1126/science.1261877. PubMed PMID:25954003 PubMed Central PMC4537935.

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. Human genomics. The human transcriptome across tissues and individuals. Science. 2015;348 (6235):660-5. doi: 10.1126/science.aaa0355. PubMed PMID:25954002 PubMed Central PMC4547472.

Foissac, S, Sammeth, M. Analysis of alternative splicing events in custom gene datasets by AStalavista. Methods Mol. Biol. 2015;1269 :379-92. doi: 10.1007/978-1-4939-2291-8_24. PubMed PMID:25577392 .

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. Nova1 is a master regulator of alternative splicing in pancreatic beta cells. Nucleic Acids Res. 2014;42 (18):11818-30. doi: 10.1093/nar/gku861. PubMed PMID:25249621 PubMed Central PMC4191425.

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. Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet. 2014;10 (8):e1004496. doi: 10.1371/journal.pgen.1004496. PubMed PMID:25121733 PubMed Central PMC4133162.

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. RNA sequencing identifies dysregulation of the human pancreatic islet transcriptome by the saturated fatty acid palmitate. Diabetes. 2014;63 (6):1978-93. doi: 10.2337/db13-1383. PubMed PMID:24379348 .

'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. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol. 2013;31 (11):1015-22. doi: 10.1038/nbt.2702. PubMed PMID:24037425 .

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. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501 (7468):506-11. doi: 10.1038/nature12531. PubMed PMID:24037378 PubMed Central PMC3918453.

Marco-Sola, S, Sammeth, M, Guigó, R, Ribeca, P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods. 2012;9 (12):1185-8. doi: 10.1038/nmeth.2221. PubMed PMID:23103880 .

Griebel, T, Zacher, B, Ribeca, P, Raineri, E, Lacroix, V, Guigó, R, Sammeth, M. Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res. 2012;40 (20):10073-83. doi: 10.1093/nar/gks666. PubMed PMID:22962361 PubMed Central PMC3488205.

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. Landscape of transcription in human cells. Nature. 2012;489 (7414):101-8. doi: 10.1038/nature11233. PubMed PMID:22955620 PubMed Central PMC3684276.

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. The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. PLoS Genet. 2012;8 (3):e1002552. doi: 10.1371/journal.pgen.1002552. PubMed PMID:22412385 PubMed Central PMC3297576.

Mundry, M, Bornberg-Bauer, E, Sammeth, M, Feulner, PG. Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS ONE. 2012;7 (2):e31410. doi: 10.1371/journal.pone.0031410. PubMed PMID:22384018 PubMed Central PMC3288049.

Gonzàlez-Porta, M, Calvo, M, Sammeth, M, Guigó, R. Estimation of alternative splicing variability in human populations. Genome Res. 2012;22 (3):528-38. doi: 10.1101/gr.121947.111. PubMed PMID:22113879 PubMed Central PMC3290788.

Montgomery, SB, Sammeth, M, Gutierrez-Arcelus, M, Lach, RP, Ingle, C, Nisbett, J, Guigo, R, Dermitzakis, ET. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 2010;464 (7289):773-7. doi: 10.1038/nature08903. PubMed PMID:20220756 PubMed Central PMC3836232.

Horner, DS, Pavesi, G, Castrignanò, T, De Meo, PD, Liuni, S, Sammeth, M, Picardi, E, Pesole, G. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief. Bioinformatics. 2010;11 (2):181-97. doi: 10.1093/bib/bbp046. PubMed PMID:19864250 .

Sammeth, M. Complete alternative splicing events are bubbles in splicing graphs. J. Comput. Biol. 2009;16 (8):1117-40. doi: 10.1089/cmb.2009.0108. PubMed PMID:19689216 .

Tilgner, H, Nikolaou, C, Althammer, S, Sammeth, M, Beato, M, Valcárcel, J, Guigó, R. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 2009;16 (9):996-1001. doi: 10.1038/nsmb.1658. PubMed PMID:19684599 .

Sammeth, M, Foissac, S, Guigó, R. A general definition and nomenclature for alternative splicing events. PLoS Comput. Biol. 2008;4 (8):e1000147. doi: 10.1371/journal.pcbi.1000147. PubMed PMID:18688268 PubMed Central PMC2467475.

Mellmann, A, Weniger, T, Berssenbrügge, C, Rothgänger, J, Sammeth, M, Stoye, J, Harmsen, D. Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms. BMC Microbiol. 2007;7 :98. doi: 10.1186/1471-2180-7-98. PubMed PMID:17967176 PubMed Central PMC2148047.

Foissac, S, Sammeth, M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res. 2007;35 (Web Server issue):W297-9. doi: 10.1093/nar/gkm311. PubMed PMID:17485470 PubMed Central PMC1933205.

Sammeth, M, Stoye, J. Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Trans Comput Biol Bioinform. ;3 (4):395-407. doi: 10.1109/TCBB.2006.46. PubMed PMID:17085848 .

Sammeth, M, Heringa, J. Global multiple-sequence alignment with repeats. Proteins. 2006;64 (1):263-74. doi: 10.1002/prot.20957. PubMed PMID:16609972 .

Sammeth, M, Griebel, T, Tille, F, Stoye, J. Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics. 2006;22 (7):889-90. doi: 10.1093/bioinformatics/btl007. PubMed PMID:16418234 .

Harmsen, D, Dostal, S, Roth, A, Niemann, S, Rothgänger, J, Sammeth, M, Albert, J, Frosch, M, Richter, E. RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. BMC Infect. Dis. 2003;3 :26. doi: 10.1186/1471-2334-3-26. PubMed PMID:14611664 PubMed Central PMC280682.

Sammeth, M, Morgenstern, B, Stoye, J. Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics. 2003;19 Suppl 2 :ii189-95. . PubMed PMID:14534189 .

Sammeth, M, Rothgänger, J, Esser, W, Albert, J, Stoye, J, Harmsen, D. QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. Bioinformatics. 2003;19 (12):1592-3. . PubMed PMID:12912847 .

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