Papers discussed in group presentations

  1. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. Yan Wei Lim, Daniel A. Cuevas, Genivaldo Gueiros Z. Silva,
Kristen Aguinaldo, Elizabeth A. Dinsdale, Andreas F. Haas,
Mark Hatay, Savannah E. Sanchez, Linda Wegley-Kelly, Bas E. Dutilh, Timothy T. Harkins, Clarence C. Lee, Warren Tom, Stuart A. Sandin, Jennifer E. Smith, Brian Zgliczynski, Mark J.A. Vermeij,
Forest Rohwer and Robert A. Edwards. PeerJ, 2014, DOI 10.7717/peerj.520
  2.  Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota. Philippe Deschamps, Yvan Zivanovic, David Moreira, Francisco Rodriguez-Valera, and Purificacio ́ n Lo ́ pez-Garcı ́a
. Genome Biology and Evolution, 2014. Toward a Census of Bacteria in Soil By Patrick D. Schloss, Jo Handelsman, pcbi (2006), Volume 2 , Issue 7
  3.  A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. Yuzhen Ye, Thomas G. Doak, pcbi (2009), Volume 5, issue 8
  4. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome. By Sahar Abubucker1, Nicola Segata2, Johannes Goll3, Alyxandria M. Schubert, Jacques Izard,
Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan,
Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methe ́, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, Curtis Huttenhower, pcbi (2012), Volume 8, Issue 6
  5. Metabolic reconstruction for metagenomic data and its application to the human microbiome. Abubucker S., Segata N., Goll J., Schubert A.M., Izard J., Cantarel B.L. . PLoS Comput Biol. 2012;8(6):e1002358.
  6. Microbial co-occurrence relationships in the human microbiome. Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. PLoS Comput Biol. 2012;8(7):e1002606. doi: 10.1371/journal.pcbi.1002606. Epub 2012 Jul 12.
  7. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. Carr R, Shen-Orr SS, Borenstein E,, PLoS Comput Biol. 2013;9(10):e1003292
  8. BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities. Shafiei M, Dunn KA, Chipman H, Gu H, Bielawski JP. (2014) PLoS Comput Biol 10(11): e1003918. doi: 10.1371/journal.pcbi.1003918
  9. Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data. Skewes-Cox, Peter; Sharpton, Thomas J.; Pollard, Katherine S.; DeRisi, Joseph L. PLoS ONE(2014), 9(8), p1
  10. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. H Bjørn Nielsen, Mathieu Almeida, Agnieszka Sierakowska Juncker, Simon Rasmussen, Junhua Li, Shinichi Sunagawa, Damian R Plichta, Laurent Gautier, Anders G Pedersen, Emmanuelle Le Chatelier, Eric Pelletier, Ida Bonde, Trine Nielsen, Chaysavanh Manichanh, Manimozhiyan Arumugam, Jean-Michel Batto, Marcelo B Quintanilha dos Santos, Nikolaj Blom, Natalia Borruel, Kristoffer S Burgdorf, Fouad Boumezbeur, Francesc Casellas, Joël Doré, Piotr Dworzynski, Francisco Guarner et al. Nature Biotechnology 32, 822–828 (2014)
  11. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. Bonnie L. Hurwitz, Anton H. Westveld, Jennifer R. Brum, and Matthew B. Sullivan. PNAS 2014 111 (29) 10714-10719, doi:10.1073/pnas.1319778111
  12. Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean. Sara A. Lincoln, Brenner Wai, John M. Eppley, Matthew J. Church, Roger E. Summons, and Edward F. DeLong. PNAS 2014 111 (27) 9858-9863; doi:10.1073/pnas.1409439111