This document provides a bibliography of sources related to exploring and mapping autoimmune disease using data and digital tools. It includes 14 sources organized under headings about the gut as an immune organ, the gut-brain axis, the microbiome, mapping the immune repertoire, and causes of autoimmune disease. The sources are peer-reviewed articles from journals such as Nature Reviews Immunology, Cell, and Gastroenterology that were accessed online between March 5-8, 2015.

1. © 2014 - All rights reserved.
Exploring and Mapping
Autoimmune Disease Using
Data and Digital Tools-
Bibliography
Bio-IT World Conference and Expo
Cambridge Healthtech Institute

2. © 2014 - All rights reserved.
Sources
• Gut as an Immune Organ
• Campbell, Andrew. "Autoimmunity and the Gut." Autoimmune Diseases (2014): n. pag.
Web. 8 Mar. 2015. http://www.hindawi.com/journals/ad/2014/152428/
• Kamada, Nobuhiko, Sang-Uk Seo, Grace Chen, and Gabriel Nüñez. "Role of the Gut
Microbiota in Immunity and Inflammatory Disease." Nature Reviews: Immunology 13
(2013): 321-35. Web. 8 Mar. 2015.
http://www.researchgate.net/publication/236337970_Role_of_the_gut_microbiota_in
_immunity_and_inflammatory_disease
• Sorini, Chiara, Marika Falcone. "Shaping the (auto)immune Response in the Gut: The
Role of Intestinal Immune Regulation in the Prevention of Type 1 Diabetes." American
Journal of Clinical Experimental Immunology (2013): 156-71. Web. 8 Mar. 2015.
<http://www.researchgate.net/publication/251876845_Shaping_the_(auto)immune_re
sponse_in_the_gut_the_role_of_intestinal_immune_regulation_in_the_prevention_of
_type_1_diabetes>.

3. © 2014 - All rights reserved.
Sources
• Gut-Brain Axis
• Mayer, Emeran, Rob Knight, Sarkis Mazmanian, John Cryan, and Kirsten Tillisch. "Gut
Microbes and the Brain: Paradigm Shift in Neuroscience." The Journal of Neuroscience
34.46 (2014): 15490-5496. Web. 8 Mar. 2015.
http://www.painresearchforum.org/papers/47412-gut-microbes-and-brain-paradigm-
shift-neuroscience
• Foster, Jane, and Karen-Anne Neufeld. "Gut-Brain Axis: How the Microbiome Influences
Anxiety and Depression." Cell 36.5 (2013): 305-38. Web. 8 Mar. 2015.
http://www.researchgate.net/publication/235404335_Gut-
brain_axis_how_the_microbiome_influences_anxiety_and_depression

4. © 2014 - All rights reserved.
Sources
• The Microbiome
• Waldor, Matthew, Gene Tyson, and Elhanan Borenstein. "Where Next for Microbiome
Research?" Public Library of Science Biology (2015): n. pag. Web. 8 Mar. 2015.
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002050
• Brüssow, Harald. "Microbiota and the Human Nature: Know Thyself." Environmental
Microbiology (2014): n. pag. Web. 8 Mar. 2015.
http://www.bionity.com/en/publications/757948/microbiota-and-the-human-nature-
know-thyself.html

5. © 2014 - All rights reserved.
Sources
• The Microbiome
• Sonnenburg, Erica, and Justin Sonnenburg. "Starving Our Microbial Self: The
Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates."
Cell Metabolism Perspective (n.d.): 779-86. Web. 8 Mar. 2015.
http://www.researchgate.net/publication/265055722_Starving_our_Microbial_Self_Th
e_Deleterious_Consequences_of_a_Diet_Deficient_in_Microbiota-
Accessible_Carbohydrates
• Kostic, Aleksandar, Ramnik Xavier, and Dirk Gevers. "The Microbiome in Inflammatory
Bowel Disease: Current Status and the Future Ahead." Gastroenterology: The Gut
Microbiome and Disease (n.d.): 1489-499. Web. 8 Mar. 2015.
http://www.gastrojournal.org/article/S0016-5085(14)00220-0/abstract

6. © 2014 - All rights reserved.
Sources
• Mapping Immune Repertoire
• Robinson, William. "Sequencing the Functional Antibody Repertoire--diagnostic and
Therapeutic Discovery." Nature Reviews: Rheumatology (2014): 1-11. Web. 8 Mar. 2015.
<http://www.bioportfolio.com/news/article/2177455/Sequencing-the-functional-
antibody-repertoire-diagnostic-and-therapeutic-discovery.html>.
• Robins, Harlan. "Immunosequencing: Applications of Immune Repertoire Deep
Sequencing." ScienceDirect (2013): 646-52. Web. 8 Mar. 2015.
http://www.researchgate.net/publication/258059445_Immunosequencing_application
s_of_immune_repertoire_deep_sequencing

7. © 2014 - All rights reserved.
Sources
• Causes of Autoimmune Disease
• Kim, Ho-Youn, Hae-Rim Kim, and Sang-Heon Lee. "Advances in Systems Biologyproaches
for Autoimmune Diseases." Immune Network 2 (2014): 73-80. PubMed Central. Web. 5
Mar. 2015. http://europepmc.org/abstract/pmc/pmc4022781
• Brodin, Petter, Vladimir Jojic, and Tianxiang Gao. "Variation in the Human Immune
System Is Largely Driven by Non-Heritable Influences." Cell 160.1-2 (2015): 37-47.
Science Direct. Web. 5 Mar. 2015.
http://www.researchgate.net/publication/271534046_Variation_in_the_human_immu
ne_system_is_largely_driven_by_non-heritable_influences
• Farth, Kyle, and Alexander Marson. "Genetic and Epigenetic Fine Mapping of Causal
Autoimmune Disease Variants." Nature 518 (2014): 337-43. Nature. Web. 5 Mar. 2015.
https://www.broadinstitute.org/publications/broad6179

8. © 2014 - All rights reserved.
Sources
• Causes of Autoimmune Disease
• Romanoski, Caset, Christopher Glass, and Hendrick Stunnenberg. "Epigenomics:
Roadmap for Regulation." Nature 518 (2015): 314-16. Nature. Web. 5 Mar. 2015.
http://europepmc.org/abstract/med/25693562
• Rojas-Villarraga, Adriana, Jenny Amaya-Amaya, and Alberto Rodriguez-Rodriguez.
"Introducing Polyautoimmunity: Secondary Autoimmune Diseases No Longer Exist."
Autoimmune Diseases 2012 (2012): n. pag. Web. 5 Mar. 2015.
http://www.oalib.com/paper/32037
• Mowat, Allan, and William Agace. "Regional Specialization Within the Intestinal Immune
System." Nature Reviews Immunology 14 (2014): 667-85. Nature. Web. 5 Mar. 2015.
http://www.pubfacts.com/detail/25234148/Regional-specialization-within-the-
intestinal-immune-system