Publications

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tyläinen Tö, Jerby L, jä EM ä, Mattila I, ntti Sä, Auvinen P, Gastaldelli A, rvinen Hä, Ruppin E, ič Mš.  2016.  Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature Communications. 7:8994.
Trivedi CM, Zhu W, Wang Q, Jia C, Kee HJin, Li L, Hannenhalli S, Epstein JA.  2010.  Hopx and Hdac2 Interact to Modulate Gata4 Acetylation and Embryonic Cardiac Myocyte Proliferation. Developmental CellDevelopmental Cell. 19
Treangen T, Messeguer X.  2009.  Novel computational methods for large scale genome comparison. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008).
Treangen T, Abraham A-L, Touchon M, Rocha EPC.  2009.  Genesis, effects and fates of repeats in prokaryotic genomes. FEMS microbiology reviews. 33:539–571.
Treangen T, Darling AE, Ragan MA, Messeguer X.  2008.  Lecture Notes in Computer ScienceBioinformatics Research and ApplicationsGapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. 4983:74-86.
Treangen T, Salzberg SL.  2011.  Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics.
Treangen T, Messeguer X.  2006.  M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC bioinformatics. 7:433.
Treangen T, Schoeler G, Phillippy AM, Bergman NH, Turell MJ.  2016.  Identification and genomic analysis of a novel group C orthobunyavirus isolated from a mosquito captured near Iquitos, Peru. PLoS Negl Trop Dis. 10:e0004440.
Treangen T, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EPC.  2009.  A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 6:180–189.
Treangen TJ, Maybank RA, Enke S, Friss MBeth, Diviak LF, Karaolis DKR, Koren S, Ondov B, Phillippy AM, Bergman NH.  2014.  Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome announcements. 2:e01110–14.
Treangen T, Rocha E.  2011.  Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 7:e1001284.
Treangen T, Sommer D.D, Angly F.E, Koren S., Pop M..  2011.  Next Generation Sequence Assembly with AMOS. Current Protocols in BioinformaticsCurrent Protocols in Bioinformatics. 11
Treangen T, Ondov BD, Koren S, Phillippy AM.  2014.  The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology. 15:524.
Treangen T, Ambur OHerman, Tonjum T, Rocha EPC.  2008.  The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome biology. 9:R60.
Treangen T, Darling A.E., Achaz G., Ragan M.A., Messeguer X., Rocha E.P.C..  2009.  A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6(2):180-189.
Treangen T, Koren S., Sommer D.D, Liu B., Astrovskaya I, Ondov B., Darling A.E, Phillippy A.M, Pop M..  2013.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome BiolGenome Biol. 14
Tootle TL, Silver SJ, Davies EL, Newman V, Latek RR, Mills IA, Selengut J., Parlikar BEW, Rebay I.  2003.  The transcription factor Eyes absent is a protein tyrosine phosphatase. NatureNature. 426
Todd GJ, Schwartz A, Rapoport F.  1989.  Management of an enlarging aortic aneurysm in the presence of radiation induced retroperitoneal fibrosis.. J Cardiovasc Surg (Torino). 30(2):233-5.
Timp W, Bravo HCorrada, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.  2014.  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.
Tilghman S., Astin H.S, Brinkley W., Chilton M.D, Cummings MP, Ehrenberg R.G, Fox M.F, Glenn K., Green P.J, Hans S. et al..  1998.  Trends in the early careers of life scientists - Preface and executive summary. Mol Biol CellMol Biol Cell. 9
Tian Y, Zhang Y, Hurd L, Hannenhalli S, Liu F, Lu MMin, Morrisey EE.  2011.  Regulation of Lung Endoderm Progenitor Cell Behavior by miR302/367. DevelopmentDevelopmentDevelopmentDevelopment. 138
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, A. Durkin S et al..  2005.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 102
Teixeira SM, El-Sayed NM, Araújo PR.  2011.  The genome and its implications.. Adv Parasitol. 75:209-30.
Taviani E, Ceccarelli D, Lazaro N, Bani S, Cappuccinelli P, Colwell RR, Colombo MM.  2008.  Environmental Vibrio spp., isolated in Mozambique, contain a polymorphic group of integrative conjugative elements and class 1 integrons. FEMS Microbiology EcologyFEMS Microbiology Ecology. 64
Taviani E, Spagnoletti M, Ceccarelli D, Haley BJ, Hasan NA, Chen A, Colombo MM, Huq A, Colwell RR.  2012.  Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae. FEBS LettersFEBS Letters.

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