Michael Sammeth

Michael Sammeth

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Michael Sammeth

Michael Sammeth

Publications by authors named "Michael Sammeth"

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35Publications

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Characterization of HPV integration, viral gene expression and E6E7 alternative transcripts by RNA-Seq: A descriptive study in invasive cervical cancer.

Genomics 2019 12 13;111(6):1853-1861. Epub 2018 Dec 13.

Genetics Program, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2018.12.008DOI Listing
December 2019

Comparative Genomics in Drosophila.

Methods Mol Biol 2018 ;1704:433-450

Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho 373, 21941-902, Rio de Janeiro, RJ, Brazil.

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http://link.springer.com/10.1007/978-1-4939-7463-4_17
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http://dx.doi.org/10.1007/978-1-4939-7463-4_17DOI Listing
December 2018

Comparative Genomics in Homo sapiens.

Methods Mol Biol 2018 ;1704:451-472

Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho 373, 21941-902, Rio de Janeiro, RJ, Brazil.

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http://link.springer.com/10.1007/978-1-4939-7463-4_18
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http://dx.doi.org/10.1007/978-1-4939-7463-4_18DOI Listing
December 2018

An automated method for detecting alternatively spliced protein domains.

Bioinformatics 2018 11;34(22):3809-3816

Molecular and Structural Biology Department, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1093/bioinformatics/bty425DOI Listing
November 2018

Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.

PLoS Negl Trop Dis 2018 10 10;12(10):e0006760. Epub 2018 Oct 10.

Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1371/journal.pntd.0006760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6179187PMC
October 2018

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

Sci Rep 2018 03 1;8(1):3877. Epub 2018 Mar 1.

Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.

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http://dx.doi.org/10.1038/s41598-018-22093-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832876PMC
March 2018

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

Methods Mol Biol 2015 ;1269:379-92

UMR1388 GenPhySE, French National Institute for Agricultural Research (INRA), Chemin de Borde Rouge, 31326, Castanet Tolosan, France.

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http://dx.doi.org/10.1007/978-1-4939-2291-8_24DOI Listing
September 2015

Human genomics. The human transcriptome across tissues and individuals.

Science 2015 May;348(6235):660-5

Center for Genomic Regulation (CRG), Barcelona, Catalonia, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Catalonia, Spain. Joint CRG-Barcelona Super Computing Center (BSC)-Institut de Recerca Biomedica (IRB) Program in Computational Biology, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1126/science.aaa0355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547472PMC
May 2015

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

PLoS Genet 2014 Aug 14;10(8):e1004496. Epub 2014 Aug 14.

University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany.

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http://dx.doi.org/10.1371/journal.pgen.1004496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133162PMC
August 2014

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

Nat Biotechnol 2013 Nov 15;31(11):1015-22. Epub 2013 Sep 15.

1] Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. [2] Netherlands Bioinformatics Centre, Leiden, The Netherlands.

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http://dx.doi.org/10.1038/nbt.2702DOI Listing
November 2013

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

Nat Methods 2012 Dec 28;9(12):1185-8. Epub 2012 Oct 28.

Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.

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http://www.nature.com/articles/nmeth.2221
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http://dx.doi.org/10.1038/nmeth.2221DOI Listing
December 2012

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

Nucleic Acids Res 2012 Nov 7;40(20):10073-83. Epub 2012 Sep 7.

Bioinformatics and Genomics Program, Centre de Regulació Genòmica (CRG), 08003 Barcelona, Spain.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gks666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488205PMC
November 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

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

PLoS One 2012 27;7(2):e31410. Epub 2012 Feb 27.

Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfaelische-Wilhelms-University, Muenster, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031410PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288049PMC
August 2012

Estimation of alternative splicing variability in human populations.

Genome Res 2012 Mar 23;22(3):528-38. Epub 2011 Nov 23.

Bioinformatics and Genomics, Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1101/gr.121947.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290788PMC
March 2012

Nucleosome positioning as a determinant of exon recognition.

Nat Struct Mol Biol 2009 Sep;16(9):996-1001

Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1038/nsmb.1658DOI Listing
September 2009

Complete alternative splicing events are bubbles in splicing graphs.

Authors:
Michael Sammeth

J Comput Biol 2009 Aug;16(8):1117-40

Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) , Barcelona, Spain.

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http://dx.doi.org/10.1089/cmb.2009.0108DOI Listing
August 2009

A general definition and nomenclature for alternative splicing events.

PLoS Comput Biol 2008 Aug 8;4(8):e1000147. Epub 2008 Aug 8.

Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1000147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2467475PMC
August 2008

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets.

Nucleic Acids Res 2007 Jul 7;35(Web Server issue):W297-9. Epub 2007 May 7.

Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkm311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933205PMC
July 2007

Comparing tandem repeats with duplications and excisions of variable degree.

IEEE/ACM Trans Comput Biol Bioinform 2006 Oct-Dec;3(4):395-407

Faculty of Technology, Bielefeld University, Germany.

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http://dx.doi.org/10.1109/TCBB.2006.46 DOI Listing
January 2007

Global multiple-sequence alignment with repeats.

Proteins 2006 Jul;64(1):263-74

Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, Amsterdam, The Netherlands.

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http://doi.wiley.com/10.1002/prot.20957
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http://dx.doi.org/10.1002/prot.20957DOI Listing
July 2006

Panta rhei (QAlign2): an open graphical environment for sequence analysis.

Bioinformatics 2006 Apr 17;22(7):889-90. Epub 2006 Jan 17.

Genome Informatics, Technical faculty, Bielefeld University, PO Box 10 01 31, 33501 Bielefeld, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btl007DOI Listing
April 2006

Divide-and-conquer multiple alignment with segment-based constraints.

Bioinformatics 2003 Oct;19 Suppl 2:ii189-95

Bielefeld University, Department of Genome Informatics, Technical Faculty, Bielefeld, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btg1077DOI Listing
October 2003