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Research interests

Np-complete problems in biology; transcription regulation, comparative regulomics, pattern recognition and large-scale genome sequencing methods.

All our research is performed in silico. Projects that require 'wet-lab' experimentation and verification, we rely on our collaborators.

Home > Research > Publications

Peer reviewed publications

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Ragnarsdóttir B, Jönsson K, Urbano A, Grönberg-Hernandez J, Lutay N, Tammi M, Gustafsson M, Lundstedt AC, Leijonhufvud I, Karpman D, Wullt B,Truedsson L, Jodal U, Andersson B, Svanborg C. "Toll-like receptor 4 promoter polymorphisms: common TLR4 variants may protect against severe urinary tract infection". PLoS One . 2010 May 20;5(5):e10734. [Locate article]

Feng Zhu, Xin Liu, Martti T. Tammi, Shengyong Yang, Yu Quan Wei and Yu Zong Chen "Identification of promising therapeutic targets in influenza genomes based on genetic, structural, physicochemical and systems profiles". Proc. Nat. Acad. Sci. Submitted 2009 [ Locate article ]

Feng Zhu, Lian Yi Han, Chan Juan Zheng, Bi Xie, Martti T. Tammi, Sheng Yong Yang, Yu Quan Wei and Yu Zong Chen "What are next generation innovative therapeutic targets? Clues from genetic, structural, physicochemical and systems profiles of successful targets". Journal of Pharmacology and Experimental Therapeutics. 2009, Jul;330(1):304-15. Epub 2009 Apr 8 [ Locate article ]

Hon Cheng Muh, Joo Chuan Tong and Martti T. Tammi "AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins". PLoS ONE 2009, Jun 10;4(6):e5861. [ Locate article ]

Joo Chuan Tong, Shen Jean Lim, Hon Cheng Muh, Fook Tim Chew, Martti T. Tammi "Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information". Bioinformatics 2009; doi: 10.1093/bioinformatics/btp077 [ Locate article ] [ Abstract ]

Chao Xie and Martti T. Tammi "CNV-seq, new method to detect copy number variation using high-throughput sequencing". BMC Bioinformatics 2009, Mar 6;10(1):80. [ Locate article ]

Shen Jean Lim, Joo Chuan Tong, Fook Tim Chew and Martti T. Tammi "The value of position-specific scoring matrices for assessment of protein allergenicity". BMC Bioinformatics 2008, Dec 12;9 12:S21. [ Locate article ]

Joo Chuan Tong, Martti T. Tammi "Prediction of protein allergenicity using local description of amino acid sequence". Frontiers in Bioscience 2008, May 1;13:6072-6078. [ Locate article ]

Joo Chuan Tong, Martti T. Tammi "Methods and protocols for the assessment of protein allergenicity and cross-reactivity". Frontiers in Bioscience 2008, Jan 1;13:4882-4888. [ Locate article ]

Arner, E., Kindlund, E., Nilsson, D., Farzana, F., Ferella, M., Tammi, M. T., Andersson, B. "Database of Trypanosoma cruzi repeated genes: 20,000 additional gene variants". BMC Genomics 2007, Oct 26:8(1):391. [ Locate article ]

Ellen Kindlund, Martti T. Tammi, Björn Andersson. Genome-Scale Rapid Alignment Tool, G-RAT. Computer Methods and Programs in Biomedicine 2007, Volume 86, Issue 1, Pages 87-92. [ Locate article ]

Thadani, R. and MT Tammi, “MicroTar: Predicting microRNA targets from nucleic acid dublexes”. BMC Bioinformatics 2006, 7, no. S20. [ Abstract ] [ html ] [ pdf ]

Zong, HZ, JLY Koh, GL Zhang, KH Choo, MT Tammi and JC Tong, “AllerTool: A Web Server for Predicting Allergenicity and Allergic Cross-Reactivity in Proteins”. Bioinformatics 2006, Feb 15;23(4):504-6. Epub 2006 Dec 6. [ Locate article ]

S Ranganathan, MT Tammi, M Gribskov and TW Tan, eds. “Establishing bioinformatics research in the asia pacific”. BMC Bioinformatics 2006, 7, no S5. [ Abstract ] [ html ] [ pdf ]

Erik Arner, Martti T. Tammi, Björn Andersson, DNPTrapper: an assembly editing tool for finishing of complex repeat regions. BMC Bioinformatics 2006, 7:155. [ Abstract ] [ html ] [ pdf ]

Tobias Allander, Martti T. Tammi, Margareta Eriksson, Annelie Bjerkner, Annika Tiveljung Lindell and Björn Andersson. Cloning of a Human Parvovirus by Molecular Screening of Respiratory Samples. Proc. Nat. Acad. Sci. 2005 Oct 25;102(43):15712-15712. 2005. Epub Oct 6. [ html ]

Tobias Allander, Martti T. Tammi, Margareta Eriksson, Annelie Bjerkner, Annika Tiveljung Lindell and Björn Andersson. Cloning of a Human Parvovirus by Molecular Screening of Respiratory Samples. Proc. Nat. Acad. Sci. 2005 Sep 6;102(36):12891-6. Epub 2005 Aug 23. [ Abstract ] [ html ] [ pdf ]

The Trypanosoma cruzi Genome Sequencing Consortium. The genome sequence of Trypanosoma cruzi, etiological agent of Chagas’ disease. Science. 2005 July 15; 309(5733): 409-15. [ Abstract ] [ html ] [ pdf ]

International Chicken Polymorphism Map Consortium. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature. 2004 Dec 9; 432(7018): 717-22. [ Abstract ] [ html ] [ pdf ]

Alvaro Rada Iglesias, Ellen Kindlund, Martti Tammi and Claes Wadelius. Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding. Gene. 2004 Oct 27; 341:149-65. - [ Locate article ]

Martti T. Tammi, Erik Arner, Björn Andersson, ReDit: Repeat Discrepancy Tagger – A Shotgun Assembly Finishing Aid. Bioinformatics. 2004 Mar. 22; 20(5):803-4. [ Abstract ] [ pdf ]

Martti T. Tammi, Erik Arner, Ellen Kindlund, Björn Andersson. Correcting Errors in Shotgun Sequences Using DNPs and a Novel Pattern Matching Algorithm. Nucleic Acids Research. 2003. 31(15): 4663-72. [ Abstract ] [ html ] [ pdf ]

Martti T. Tammi, Erik Arner, Björn Andersson. TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences. Computer Methods and Programs in Biomedicine. 2003. 70: 47-59. [ Locate article ]

Martti T. Tammi, Erik Arner, Tom Britton, Björn Andersson. Separation of Nearly Identical Repeats in Shotgun Assemblies using Defined Nucloetide Positions, DNPs. Bioinformatics. 2002. 18(3): 37988. [ Abstract ] [ pdf ]

Cavelier L, Erikson I, Tammi M, Jalonen P, Lindholm E, Jazin E, Smith P, Luthman H, Gyllensten U. MtDNA mutations in maternally inherited diabetes: presence of the 3397 ND1 mutation previously associated with Alzheimer’s and Parkinson’s disease. Hereditas. 2001. 135(1): 65-70. [ Abstract ] [ pdf ]

Win Degrave, AnhNhi Tran, Martti T. Tammi, Daniel Sanchez, Martin Aslett. The Trypanosoma cruzi Genome Initiative on the Web. Trends in Parasitology. Mar 2001. 17(3): 1545. [ Abstract ] [ html ] [ pdf ]

Betina M. Porcel , AnhNhi Tran, Martti T. Tammi , Zoltan Nyarady, Maria Rydåker, Turan P. Urmenyi, Edson Rondinelli, Ulf Pettersson, Björn Andersson, Lena Åslund. Gene survey of the pathogenic protozoan Trypanosoma cruzi. Genome Research. Aug 2000. 10(8): 11037. [ Abstract ] [ html ] [ pdf ]

Björn Andersson , Lena Åslund , Tammi M, AnhNhi Tran , Jörg D. Hoheisel, Ulf Pettersson. Complete sequence of a 93.4kb contig from chromosome 3 of Trypanosoma cruzi containing a strandswitch region. Genome Research. Aug 1998. 8(8): 80916. [ Abstract ] [ html ] [ pdf ]

Book Chapters

Björn Andersson and Martti T. Tammi. Algorithms for sequence errors, chapter in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Adam Kuspa Ed. John Wiley & Sons LTD, 2005. ISBN-10: 0470849746, ISBN-13: 978-0470849743.

Martti T. Tammi and Björn Andersson. Errors in sequence assembly and corrections, chapter in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Adam Kuspa Ed. John Wiley & Sons LTD, 2005. ISBN-10: 0470849746, ISBN-13: 978-0470849743.

TW Tan, Justin KH Choo, Victor Tong, VB Bajic and Martti T. Tammi. Biological Databases and Web Services: Metrics for Quality, chapter in Information Processing and Living Systems , World Scientific, 2004. ISBN 978-1-86094-563-2.