B1;2c Todd J. Treangen, Ph.D.

Todd J. Treangen, Ph.D.


Senior Bioinformatics Scientist
National Biodefense Analysis and Countermeasures Center
E-mail: treangen
Phone: 443-287-8782
Fax: 410-955-0958
Twitter: @traingene

Affiliations:
Center for Bioinformatics and Computational Biology
Computer Science Department, University of Maryland

 

Background

Research

My current research interests include efficient multiple genome alignment, phylogenomics, population genetics, meta(zoan,genomic) genome assembly and comparative human genomics/genetics, mostly via NGS data. I've also participated in the Genome Assembly Gold-Standard Evalutions (GAGE). My historical research interests include developing efficient algorithms and tools to detect and classify unique and repeated DNA sequence in genomes, resulting in two software tools: M-GCAT and Repeatoire. I received my MSc and PhD degrees in Computer Science from the Department of Software, Technical University of Catalonia, Barcelona, Spain under the guidance of my PhD supervisor Prof. Xavier Messeguer.

Publications & Conferences

Google , PubMed

Journals:

Sorted by # of citations (as of August 29th 2012)

  1. Treangen, T.; Messeguer, X.; "M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species",BMC bioinformatics,7,1,433,2006,BioMed Central Ltd
  2. Treangen, T.J.; Rocha, E.P.C.; "Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes",PLoS Genetics,7,1,e1001284,2011,Public Library of Science
  3. Treangen, T.J.; Abraham, A.L.; Touchon, M.; Rocha, E.P.C.; "Genesis, effects and fates of repeats in prokaryotic genomes",FEMS microbiology reviews,33,3,539-571,2009,Wiley Online Library
  4. Treangen, T.J.; Ambur, O.H.; Tonjum, T.; Rocha, EP; "The impact of the neisserial DNA uptake sequences on genome evolution and stability",Genome Biol,9,3,R60,2008,
  5. Darling, A.E.; Treangen, T.J.; Messeguer, X.; Perna, N.T.; "Analyzing patterns of microbial evolution using the mauve genome alignment system",METHODS IN MOLECULAR BIOLOGY,396,,135,2007,Springer
  6. Human Microbiome Project Consortium; "Structure, function and diversity of the healthy human microbiome",Nature,486,7402,207-14,2012,
  7. Salzberg, S.L.; Phillippy, A.M.; Zimin, A.; Puiu, D.; Magoc, T.; Koren, S.; Treangen, T.J.; Schatz, M.C.; Delcher, A.L.; Roberts, M.; "GAGE: A critical evaluation of genome assemblies and assembly algorithms,Genome Research",22,3,557-567,2012,Cold Spring Harbor Lab
  8. Darling, A.; Treangen, T.; Zhang, L.; Kuiken, C.; Messeguer, X.; Perna, N.; "Procrastination leads to efficient filtration for local multiple alignment",Algorithms in Bioinformatics,126-137,2006,Springer
  9. Treangen, T.J.; Salzberg, S.L.; "Repetitive DNA and next-generation sequencing: computational challenges and solutions",Nature Reviews Genetics,2011,Nature Publishing Group
  10. Human Microbiome Project Consortium; "A framework for human microbiome research",Nature,486,7402,215-21,2012
  11. Koren, S.; Treangen, T.J.; Pop, M.; "Bambus 2: scaffolding metagenomes,Bioinformatics",27,21,2964-2971,2011,Oxford Univ Press
  12. Liu, B.; Gibbons, T.; Ghodsi, M.; Treangen, T.; Pop, M.; "Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences",BMC Genomics,12,Suppl 2,S4,2011,BioMed Central Ltd
  13. Treangen, T.J.; Darling, A.E.; Achaz, G.; Ragan, M.A.; Messeguer, X.; Rocha, E.P.C.; "A novel heuristic for local multiple alignment of interspersed DNA repeats",IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB),6,2,180-189,2009,IEEE Computer Society Press
  14. Treangen, T.J.; Sommer, D.D.; Angly, F.E.; Koren, S.; Pop, M.; "Next Generation Sequence Assembly with AMOS,Current Protocols in Bioinformatics",11,,1-11.8,2011,Wiley Online Library
  15. Enk, J.; Devault, A.; Debruyne, R.; King, C.; Treangen, T.; O'Rourke, D.; Salzberg, S.; Fisher, D.; MacPhee, R.; Poinar, H.; "Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths",Genome Biology [Internet],12,,R51,2011,
  16. Huttenhower, C.; Gevers, D.; Knight, R.; Abubucker, S.; Badger, J.H.; Chinwalla, A.T.; Creasy, H.H.; Earl, A.M.; Fitzgerald, M.G.; Fulton, R.S.; "Structure, function and diversity of the healthy human microbiome",Nature,486,,207-214,2012,
  17. Liu, B.; Faller, L.L.; Klitgord, N.; Mazumdar, V.; Ghodsi, M.; Sommer, D.D.; Gibbons, T.R.; Treangen, T.J.; Chang, Y.C.; Li, S.; "Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease",PloS one,7,6,e37919,2012,Public Library of Science

Conferences:

  1. Todd J Treangen, Aaron E. Darling, Mark A. Xavier Messeguer. Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. Lecture Notes in Bioinformatics 4983. pp. 74–86, 2008. c Springer-Verlag Berlin Heidelberg 2008. [PDF]
  2. Todd J Treangen, Nilesh Modi, and Xavier Messeguer. Optimized search for common unique substrings, on both forward and reverse strands, in multiple DNA sequences. Poster proceedings of the 1st internation conference on Bioinformatics Research and Development (BIRD'07).
  3. Aaron E Darling, Todd J Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna. Procrastination leads to efficient filtration for local multiple alignment. WABI 2006. Lecture Notes in Bioinformatics 4175, Springer-Verlag 2006. [PDF]

Service

  • Peer reviewer: Bioinformatics, BMC Bioinformatics, Genome Research, Nucleic Acids Research, Nature Methods, PLoS ONE, PLoS Genetics
  • Program committee member: ACM/BCB, ICABBS, RECOMB-CG