CMSC 828G: Bioinformatics for Metagenomics

Reading list, Fall 2009

All of these papers are available for download here:


1.  The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet.
Committee on Metagenomics: Challenges and Functional Applications, National Research Council
ISBN: 978-0-309-10676-4, 170 pages, 6 x 9, paperback (2007)
Executive Summary

2.  The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
Committee on Metagenomics: Challenges and Functional Applications, National Research Council
ISBN: 978-0-309-10676-4, 170 pages, 6 x 9, paperback (2007)
Report in Brief

3.  Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes.
Jonathan A. Eisen
PLoS Biol 5(3): e82 (2007). doi:10.1371/journal.pbio.0050082

4.  Microbiology: Metagenomics
Philip Hugenholtz and Gene W. Tyson
Nature 455, 481-483 (25 September 2008) | doi:10.1038/455481a; Published online 24 September 2008

Metagenomics studies and reviews (with methods mixed in)

5.  Uncultured soil bacteria are a reservoir of new antibiotic resistance genes
C. S. Riesenfeld, R. M. Goodman and J. Handelsman
Environmental Microbiology (2004) 6(9), 981–989 doi:10.1111/j.1462-2920.2004.00664.x

6.  Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
James Robert White, Niranjan Nagarajan, Mihai Pop
PLoS Comput Biol 5(4): e1000352. doi:10.1371/journal.pcbi.1000352

7.  Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
Hendrik N. Poinar, Carsten Schwarz, Ji Qi, Beth Shapiro, Ross D. E. MacPhee, Bernard Buigues, Alexei Tikhonov, Daniel H. Huson, Lynn P. Tomsho, Alexander Auch, Markus Rampp, Webb Miller, Stephan C. Schuster
Science 20 January 2006: Vol. 311. no. 5759, pp. 392 - 394  DOI: 10.1126/science.1123360

8.  Genomic studies of uncultivated Archaea
Christa Schleper, German Jurgens and Melanie Jonuscheit
Nature Reviews Microbiology, Vol. 3, June 2005, 479.

9.  Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter et al.
Science 304, 66 (2004).

10. Genomic analysis of uncultured marine viral communities
Mya Breitbart, Peter Salamon, Bjarne Andresen, Joseph M. Mahaffy, Anca M. Segall, David Mead, Farooq Azam, and Forest Rohwer.
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5.

11. The Metagenomics of Soil
Rolf Daniel
Nature Reviews Microbiology, Vol. 3, June 2005, 470.

12. Microbial Community Genomics in the Ocean
Edward F. DeLong
Nature Reviews Microbiology, Vol. 3, June 2005, 459.

13, Viral metagenomics
Robert A. Edwards and Forest Rohwer
Nature Reviews Microbiology, Vol. 3, June 2005, 504.

14. Human gut microbes linked to obesity.
Ley, R.E., Turnbaugh, P.J., Klein, S., and Gordon, J.I. 
Nature 444:1022–1023 (2006).

15. Metagenomic Analysis of the Human Distal Gut Microbiome
Steven R. Gill, Mihai Pop, Robert T. DeBoy, Paul B. Eckburg, Peter J. Turnbaugh, Buck S. Samuel, Jeffrey I. Gordon, David A. Relman, Claire M. Fraser-Liggett, Karen E. Nelson
Science 312, 1355 (2006).

16. Geobiology of a microbial endolithic community in the Yellowstone geothermal environment
Jeffrey J. Walker, John R. Spear & Norman R. Pace
Nature 434 | 21 APRIL 2005 |

17. Community Genomics in Microbial Ecology and Evolution
Eric E. Allen and Jillian F. Banfield
Nature Reviews Microbiology, Vol. 3, June 2005, 489.

18. Community structure and metabolism through reconstruction of microbial genomes from the environment
Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, Paul M. Richardson, Victor V. Solovyev,
Edward M. Rubin, Daniel S. Rokhsar & Jillian F. Banfield
Nature 428 | 4 MARCH 2004 |

19. RNA Viral Community in Human Feces:  Prevalence of Plant Pathogenic Viruses
Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh,
Martin L. Hibberd, Edison T. Liu, Forest Rohwer, Yijun Ruan
PLoS Biology | 0108 January 2006 | Volume 4 | Issue 1 | e3.

20. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI
An obesity-associated gut microbiome with increased capacity for energy harvest. 
[] webcite
Nature 2006, 444(7122):1027-1031

21. Elizabeth A. Grice, Heidi H. Kong, Gabriel Renaud, et al.
A diversity profile of the human skin microbiota.
Genome Res. 2008 18: 1043-1050.

Bioinformatics methods papers

1. Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
Chen K, Pachter L
PLoS Comput Biol 1(2): e24 (2005).  doi:10.1371/journal.pcbi.0010024

2. MEGAN analysis of metagenomic data
Daniel H. Huson, Alexander F. Auch, Ji Qi, and Stephan C. Schuster
Genome Res. 2007 17: 377-386

3. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
Arthur Brady & Steven L Salzberg
Nature Methods published online 2 August 2009; doi:10.1038/NMETH.1358.

4. How do we compare hundreds of bacterial genomes?
Dawn Field, Gareth Wilson and Christopher van der Gast
Current Opinion in Microbiology 2006, 9:499–504

5. Building on basic metagenomics with complementary technologies
Falk Warnecke and Philip Hugenholtz
Genome Biology 2007, 8:231doi:10.1186/gb-2007-8-12-231

6. Visual and statistical comparison of metagenomes
Suparna Mitra, Bernhard Klar and Daniel H. Huson
Bioinformatics Vol. 25 no. 15 2009, pages 1849–1855.

7. A Bioinformatician’s Guide to Metagenomics (very long)
Victor Kunin, Alex Copeland Alla Lapidus, Konstantinos Mavromatis, and Philip Hugenholtz
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, Dec. 2008, p. 557–578 Vol. 72, No. 4 doi:10.1128/MMBR.00009-08

8. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
K. Mavromatis et al.
Nature Methods - 4, 495 - 500 (2007)
Published online: 29 April 2007; | doi:10.1038/nmeth1043

9. CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads
Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, Jonathan A Eisen

10. Metagenomics: Read length matters
K. Eric Wommack, Jaysheel Bhavsar, and Jacques Ravel
Appl. Environ. Microbiol. March 2008, p. 1453-1463, Vol. 74, No. 5

11. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
Micah Hamady and Rob Knight
Genome Research (2009) 19: 1141-1152

12. Accurate phylogenetic classification of variable-length DNA fragments
Alice Carolyn McHardy, Héctor García Martín, Aristotelis Tsirigos, Philip Hugenholtz & Isidore Rigoutsos
Nature Methods - 4, 63 - 72 (2007)
Published online: 10 December 2006; | doi:10.1038/nmeth976

13. Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
C. von Mering, P. Hugenholtz, J. Raes, S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward, P. Bork
Science 23 February 2007: Vol. 315. no. 5815, pp. 1126 - 1130
DOI: 10.1126/science.1133420

14. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
Patrick D Schloss and Jo Handelsman
BMC Bioinformatics 2008, 9:34doi:10.1186/1471-2105-9-34

15. Quantitative assessment of protein function prediction from metagenomics shotgun sequences
E. D. Harrington, A. H. Singh, T. Doerks, I. Letunic, C. von Mering, L. J. Jensen, J. Raes, and P. Bork
Proc. Natl. Acad. Sci. 104:35 (2007), 13913-13918

16. Methods for comparative metagenomics
Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch and Stephan C Schuster
BMC Bioinformatics 2009, 10(Suppl 1):S12 doi:10.1186/1471-2105-10-S1-S12

17. Prediction of effective genome size in metagenomic samples. 
Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P.
Genome Biol 2007, 8:R10.

18. Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics.
Kasper Munch et al.
Systematic Biology, 57:5 (2008), 750—757.

19. Fast phylogenetic DNA barcoding
Kasper Munch, Wouter Boomsma, Eske Willerslev and Rasmus Nielsen.
Phil. Trans. R. Soc. B (2008) 363, 3997–4002.

20. Noguchi H, Park J, Takagi T: MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic acids research 2006, 34(19):5623-5630.

21. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP et al: A core gut microbiome in obese and lean twins. Nature 2009, 457(7228):480-484.

22. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5(3): e77. doi:10.1371/journal.pbio.0050077.

23. Chon-Kit Kenneth Chan,1 Arthur L. Hsu,1 Sen-Lin Tang,2 and Saman K. Halgamuge. Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing. Journal of Biomedicine and Biotechnology (2008), Article ID 513701, doi:10.1155/2008/513701.