Online supplements to print publications

Chung H, et al., (2012). Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota. Cell.
[Online Supplement]

Pamp SJ, et al. (2012) Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Research, June 22(6):1107-1119.
[Electronic version][Online Supplement]

Bik EM, et al. (2006) 
Molecular analysis of the bacterial microbiota in the human stomach. PNAS 103(3): 732-737.
[Electronic version] [FASTA file with all 1833 clone insert sequences] [FASTA file with the 128 OTU representatives] [OTU table][Supplemental Table 3]

Cummings, et al. (2006) Species- and Strain-Specific Control of a Complex, Flexible Regulon by BordetellaBvgAS. J Bacteriol., 188(5), 1775-85. 
[Electronic version] [Online Supplement]

Palmer, et al. (2006) Rapid quantitative profiling of complex microbial populations.Nucleic Acids Res, 34(1), e5.
[Electronic version and online supplement]

Bik EM, et al. (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A, 103(3), 732-7.
[Electronic version and online supplement]

Diavatopoulos, et al (2005) Bordetella pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchisepticaPLoS Pathog., 1(4), e45.
[Electronic version and online supplement]

Griffiths, et al. (2005) Genomewide Analysis of the Host Response to Malaria in Kenyan Children. Journal of Infectious Diseases, 191, 1599-1611.
[ Electronic version and online supplement]

Eckburg, et al. (2005) Diversity of the Human Intestinal Microbial Flora. Science, 308(5728), 1635-1638.
[ Electronic version (Science)] [Download sequence data (ARB database, OTU spreadsheet, and FASTA file)] [Supporting Online Material]

Cummings C, et al. (2004). Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J. Bacteriol 186(5):1484-92. [Link to publication] [Supplemental Material]

Belcher CE et al. (2000), The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies, PNAS. [Link to publication] [Link to Supplemental]

Some of these links might not work. I tried to copy/paste information and links from our old website and Asiago server, but unfortunately, this did not always work. If you cannot find a supplement on this page, please go to the supplements page of our old website at
If you still cannot find the information you look for, please contact me (Elies Bik) at eliesbik AT stanford dot edu, and I will try to help.