Bridging the Autoimmune Abyss through New Discoveries

© 2015 - All rights reserved.
Bonnie Feldman DDS MBA
Priya Sahdev
Tiffany Simms
Bridging the Autoimmune Abyss
through New Discoveries

Bridging the Autoimmune Abyss through
New Discoveries
+1.310.666.5312
drbonnie360@gmail.com
www.drbonnie360.com
@DrBonnie360
www.facebook.com/YourAutoimmunityConnection
Bonnie Feldman, DDS, MBA
Business Development for Digital Health
Priya Sahdev, BS
UCLA Class of 2016
Microbiology, Immunology,
& Molecular Genetics
Tiffany Simms, BS
UCLA Class of 2015
Anthropology

The Invisible Epidemic: Incidence & Prevalence
• Feldman, Bonnie. “Why is Autoimmune Disease Under-served.” Slideshare (2015).
http://bit.ly/1B57pNb
• Groza, Tudor et al. “The Human Phenotype Ontology: Semantic Unification of Common and
Rare Disease.” The American Journal of Human Genetics (2015). http://www.irdirc.org/the-
human-phenotype-ontology-semantic-unification-of-common-and-rare-disease/
• Nakazawa Jackson, Donna. The Autoimmune Epidemic. New York: A Touchstone Book, 2008.
Print
• “More than 450 Medicines in Development for Rare Diseases.” Medicines in Development
(2013). http://phrma.org/Medicines-Development-Rare-Diseases

Basic Science Foundation for Discovery

New Discovery Fuels Collaboration: Immunology
& Repertoire Sequencing
• Burton, Bronwen et al. “Sequential transcriptional changes dictate safe and effective
antigen-specific immunotherapy.” Nature Communications (2014).
http://scholar.qsensei.com/content/1yq4qh
• Norman, Jason et al. “Disease-Specific Alterations in the Enteric Virome in Inflammatory
Bowel Disease.” Cell (2015). http://f1000.com/prime/725326230
• Poletaev et al. “Immunophysiology versus immunopathology: Natural autoimmunity in
human health and disease.” Pathophysiology 19.3 (2012): 221-
231.<http://www.researchgate.net/publication/230655913_Immunophysiology_versus_im
munopathology_Natural_autoimmunity_in_human_health_and_disease

• Ramesh, Manish et al. “Clonal and Constricted T cell repertoire in Common Variable
Immune Deficiency.” Clinical immunology (Orlando, Fla.) (2015).
http://www.bioportfolio.com/resources/pmarticle/1148910/Clonal-and-Constricted-T-cell-
repertoire-in-Common-Variable-Immune-Deficiency.html
• Robins, Harlan. “Immunosequencing: applications of immune repertoire deep sequencing.”
Current Opinion in Immunology 25.5 (2013): 646–52.
http://www.researchgate.net/publication/258059445_Immunosequencing_applications_of
_immune_repertoire_deep_sequencing

• Robinson, William. “Sequencing the functional antibody repertoire—diagnostic and
therapeutic discovery.” Nature Reviews Rheumatology 11.3 (2015): 171–182.
http://www.pubfacts.com/detail/25536486/Sequencing-the-functional-antibody-
repertoire-diagnostic-and-therapeutic-discovery
• Spreafico, Roberto et al. “A circulating reservoir of pathogenic-like CD4+ T cells shares a
genetic and phenotypic signature with the inflamed synovial micro-environment.” Annals of
the Rheumatic Diseases (2014): annrheumdis–2014–206-226.
http://www.researchgate.net/publication/269719321_A_circulating_reservoir_of_pathoge
nic-
like_CD4_T_cells_shares_a_genetic_and_phenotypic_signature_with_the_inflamed_synovi
al_micro-environment

Polyautoimmunity: No Longer Organ Specific
• Castiblanco, John, Mauricio Arcos-Burgos, and Juan-Manuel Anaya. “What is next after the
genes for autoimmunity?” BMC Medicine 11 (2013): 197.
http://www.biomedcentral.com/1741-7015/11/197
• Franco, -S, and -M Anaya. “The autoimmune tautology with a focus on antiphospholipid
syndrome.” Lupus 23.12 (2014): 1273-1275.
http://www.researchgate.net/publication/265733380_The_autoimmune_tautology_with_a
_focus_on_antiphospholipid_syndrome
Rare Disease.” The American Journal of Human Genetics (2015). http://www.irdirc.org/the-
human-phenotype-ontology-semantic-unification-of-common-and-rare-disease/

Polyautoimmunity: No Longer Organ Specific
• Greenwood, Veronique. “Disease Networks Show Molecular Connections." Quanta
Magazine” (2015). https://www.quantamagazine.org/20150129-networks-reveal-the-
connections-of-disease/
• Zippi, Maddalena. “Extraintestinal manifestations in a large series of Italian inflammatory
bowel disease patients.” World Journal of Gastroenterology 20.46 (2014): 17463-
17467.http://docrchive.com/document/extraintestinal-manifestations-in-a-large-series-of-
italian-inflammatory-bowel-disease-patients-7348008145211277/

Personal Trial and Error: Treatments & Therapies
• Bot, Adrian et al. “Target discovery for T cell therapy: next steps to advance
Immunotherapies.” Journal for Immunotherapy of Cancer (2015).
http://www.immunotherapyofcancer.org/content/pdf/s40425-015-0061-5.pdf
• Burton, Bronwen et al. “Sequential transcriptional changes dictate safe and effective
antigen-specific immunotherapy.” Nature Communications (2014). http://research-
information.bristol.ac.uk/en/publications/sequential-transcriptional-changes-dictate-safe-
and-effective-antigenspecific-immunotherapy(8e1716fd-8874-45eb-84a9-
0dc5540e26a8)/export.html
• Chang, Christopher. “Unmet needs in the treatment of autoimmunity: From aspirin to stem
cells.” Autoimmunity Reviews 13 (2014).
http://www.researchgate.net/publication/259917083_Unmet_Needs_in_the_Treatment_o
f_Autoimmunity_From_Aspirin_to_Stem_Cells

• Curatola, Gerard. “Oral Microbiome Homeostasis: The New Frontier in Oral Care Therapies.”
Symbiosis (2013):1-3. http://www.symbiosisonlinepublishing.com/dentistry-oraldisorders-
therapy/dentistry-oraldisorders-therapy05.php
• Gertner, Jon. “What’s Lurking In Your Microbiome? Possibly, a Cure for Disease.” Fast
Company (2015). http://www.fastcompany.com/3039891/gut-check
Print.
• Olle, Bernat. “Medicines from microbiota.” Nature Biotechnology 31.4 (2013): 309-315.
http://www.researchgate.net/publication/236128149_Medicines_from_microbiota

• Petrof et al. “Microbial ecosystems therapeutics: a new paradigm in medicine?” Beneficial
microbes 4.1 (2013): 53-65.
http://www.researchgate.net/publication/233963283_Microbial_ecosystems_therapeutics
_A_new_paradigm_in_medicine
• Sabatos-Peyton, Catherine A, Johan Verhagen, and David C Wraith. “Antigen-specific
immunotherapy of autoimmune and allergic diseases.” Current opinion in immunology 22.5
(2010): 609–15. http://www.researchgate.net/publication/46305185_Antigen-
specific_immunotherapy_of_autoimmune_and_allergic_diseases
• Velasquez-Manoff, Moises. An Epidemic of Absence. New York: Scribner, 2012. Print.

Treatments & Therapies: Fecal Microbiota
Transplants
• Borody, Thomas, and Alexander Khoruts. “Fecal microbiota transplantation and emerging
applications.” Nature Reviews Gastroenterology and Hepatology 9.2 (2011): 88–96.
http://www.researchgate.net/publication/51901488_Borody_TJ_Khoruts_A.._Fecal_microb
iota_transplantation_and_emerging_applications._Nat_Rev_Gastroenterol_Hepatol_9_88-
96
• Brüssow, Harald. “Microbiota and the human nature: know thyself.” Environmental
Microbiology 17.1 (2015): 10–15.
http://www.researchgate.net/publication/269727325_Microbiota_and_the_human_nature
_know_thyself

Treatments & Therapies: Fecal Microbiota
Transplants
• Petrof, Elaine, and Alexander Khoruts. “From stool transplants to next-generation
microbiota therapeutics.” Gastroenterology 146.6 (2014): 1573-1582.
http://www.researchgate.net/publication/259698247_From_Stool_Transplants_to_Next-
generation_Microbiota_Therapeutics
• Scher, Jose et al. “Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in
Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease.”
Arthritis & Rheumatology 67.1 (2015): 128–139.
http://www.researchgate.net/publication/266974816_Decreased_Bacterial_Diversity_Char
acterizes_the_Altered_Gut_Microbiota_in_Patients_With_Psoriatic_Arthritis_Resembling_
Dysbiosis_in_Inflammatory_Bowel_Disease

Treatments & Therapies: Prebiotics and Probiotics
• Bindels, Laure et al. “Towards a more comprehensive concept for prebiotics.” Nature
Reviews Gastroenterology & Hepatology (2015).
http://www.researchgate.net/publication/274319084_Towards_a_more_comprehensive_c
oncept_for_prebiotics
• Derrien, Muriel, and Johan Vlieg. “Fate, activity, and impact of ingested bacteria within the
human gut microbiota.” Trends in Microbiology (2015).
http://www.researchgate.net/publication/274405159_Fate_activity_and_impact_of_ingest
ed_bacteria_within_the_human_gut_microbiota
• Vieira, Angélica, Mauro Teixeira, and Flaviano Martins. “The Role of Probiotics and
Prebiotics in Inducing Gut Immunity.” Frontiers in Immunology 4 (2013): 445.
http://www.researchgate.net/publication/259492313_The_Role_of_Probiotics_and_Prebio
tics_in_Inducing_Gut_Immunity

The Microbiome Lifeline
• Ackerman, Jennifer. “The Ultimate Social Network.” Scientific American 306.6 (2012): 36–43.
http://www.researchgate.net/publication/225084801_The_ultimate_social_network
• Brusca, Samuel, Steven Abramson, and Jose Scher. “Microbiome and mucosal inflammation as
extra-articular triggers for rheumatoid arthritis and autoimmunity.” Current Opinion in
Rheumatology (2014).
http://www.researchgate.net/publication/258700816_Brusca_S.B._Abramson_S.B.__Scher_J.U.
_Microbiome_and_mucosal_inflammation_as_extra-
articular_triggers_for_rheumatoid_arthritis_and_autoimmunity._Curr._Opin._Rheumatol._26_1
01-107
• Brüssow, Harald. “Microbiota and the human nature: know thyself.” Environmental Microbiology
17.1 (2015): 10–15.
http://www.researchgate.net/publication/269727325_Microbiota_and_the_human_nature_kn
ow_thyself

• Garrett, Wendy. “From cell biology to the microbiome: An intentional infinite loop.” The
Journal of Cell Biology (2015).
http://www.researchgate.net/publication/279862421_From_cell_biology_to_the_microbio
me_An_intentional_infinite_loop
• Hevia, Arancha et al. “Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus.”
mBio (2014).
http://www.academia.edu/13411926/Intestinal_dysbiosis_associated_with_systemic_lupus
_erythematosus
• Kamada, Nobuhiko et al. “Role of the gut microbiota in immunity and inflammatory
disease.” Nature Reviews Immunology 13.5 (2013): 321–335.
http://www.researchgate.net/publication/236337970_Role_of_gut_microbiota_in_immuni
ty_and_inflammatory_disease

• Proal, Amy, Paul Albert, and Trevor Marshall. “Inflammatory disease and the human
microbiome.” Discovery medicine 17.95 (2014): 257–65.
http://www.researchgate.net/publication/262782132_Inflammatory_disease_and_the_hu
man_microbiome
• “Modern Medicine: Microbes Maketh Man." The Economist, (2012).
http://www.economist.com/node/21560559
• Waldor, Matthew et al. “Where next for microbiome research?” PLoS biology 13.1 (2015).
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002050
• Yurkovetskiy, Leonid, Joseph Pickard, and Alexander Chervonsky. “Microbiota and
Autoimmunity: Exploring New Avenues.” Cell Host & Microbe (2015).
http://scifeeds.com/journal-article/microbiota-and-autoimmunity-exploring-new-avenues/

The Microbiome Lifeline: Gut As An Organ of
Immunity
• Campbell, Andrew. “Autoimmunity and the Gut.” Autoimmune Diseases 2014 (2014): 152-428.
http://www.researchgate.net/publication/262886119_Autoimmunity_and_the_Gut
• Goldszmid, Romina, and Giorgio Trinchieri. “The price of immunity.” Nature Immunology 13.10
(2012): 932–8. http://www.researchgate.net/publication/230879962_The_price_of_immunity
• Kamada, Nobuhiko et al. “Role of the gut microbiota in immunity and inflammatory disease.”
Nature Reviews Immunology 13.5 (2013): 321–335.
http://www.researchgate.net/publication/236337970_Role_of_gut_microbiota_in_immunity_a
nd_inflammatory_disease
• Kohn, David. “Joint Pain, From the Gut.” The Atlantic (2015).
http://www.theatlantic.com/health/archive/2015/01/joint-pain-from-the-gut/383772/

Immunity
• Mowat, Allan, and William Agace. “Regional specialization within the intestinal immune
system.” Nature Reviews Immunology 14.10 (2014): 667–85.
http://www.researchgate.net/publication/265862048_Regional_specialization_within_the_
intestinal_immune_system
• Sorini, Chiara, and 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 and experimental immunology 2.2 (2013): 156–71.
http://www.researchgate.net/publication/251876845_Shaping_the_(auto)immune_respon
se_in_the_gut_the_role_of_intestinal_immune_regulation_in_the_prevention_of_type_1_
diabetes

Immunity
• Strober, Warren. “Impact of the gut microbiome on mucosal inflammation.” Trends in
Immunology (2013).
http://www.researchgate.net/publication/255984931_Impact_of_the_gut_microbiome_on
_mucosal_inflammation
• Yurkovetskiy, Leonid, Joseph Pickard, and Alexander Chervonsky. “Microbiota and
Autoimmunity: Exploring New Avenues.” Cell Host & Microbe (2015).
http://www.researchgate.net/publication/276358904_Microbiota_and_Autoimmunity_Expl
oring_New_Avenues

The Microbiome Lifeline: Gut-Brain Axis
• Alcock, Joe, Carlo Maley, and Athena Aktipis. “Is eating behavior manipulated by the
gastrointestinal microbiota? Evolutionary pressures and potential mechanisms.” BioEssays
(2014). https://ucsf.box.com/shared/static/pdz2z4b5fdvwlpr9hfdh.pdf
• Brod, Samuel et al. “‘As above, so below’ examining the interplay between emotion and the
immune system.” Immunology 143.3 (2014): 311–8.
http://www.researchgate.net/publication/263291162_As_above_so_below_Examining_the
_interplay_between_emotion_and_the_Immune_System
• Forsythe, Paul et al. “Mood and gut feelings.” Brain, Behavior, and Immunity (2010).
http://www.journals.elsevier.com/brain-behavior-and-immunity/

• Foster, Jane, and Karen-Anne Neufeld. “Gut–brain axis: how the microbiome influences
anxiety and depression.” Trends in Neurosciences (2013).
http://www.researchgate.net/publication/235404335_Gut-
brain_axis_How_the_microbiome_influences_anxiety_and_depression
• Hadhazy, Adam. “Think Twice: How the Gut’s ‘Second Brain’ Influences Mood and Well-
Being." Scientific American (2010). http://www.scientificamerican.com/article/gut-second-
brain/
• Mayer, Emeran et al. “Gut Microbes and the Brain: Paradigm Shift in Neuroscience.” The
Journal of Neuroscience (2014).
http://www.researchgate.net/publication/268233441_Gut_Microbes_and_the_Brain_Para
digm_Shift_in_Neuroscience

• O’Mahony et al. “Serotonin, tryptophan metabolism and the brain-gut-microbiome axis.”
Behavioural Brain Research 277 (2015): 3248.
http://www.researchgate.net/publication/264389028_Serotonin_Tryptophan_Metabolism_
and_the_Brain-Gut-_Microbiome_Axis
• Steenbergen, Laura et al. “A randomized controlled trial to test the effect of multispecies
probiotics on cognitive reactivity to sad mood.” Brain, Behavior, and Immunity (2015).
http://www.researchgate.net/publication/274781872_A_randomized_controlled_trial_to_t
est_the_effect_of_multispecies_probiotics_on_cognitive_reactivity_to_sad_mood

The Microbiome Lifeline: Fixing Your Leaky Gut is Key
• Derrien, Muriel, and Johan Vlieg. “Fate, activity, and impact of ingested bacteria within the
human gut microbiota.” Trends in Microbiology (2015).
http://www.researchgate.net/publication/274405159_Fate_activity_and_impact_of_ingested_
bacteria_within_the_human_gut_microbiota
• Fasano, Alessio. “Leaky gut and autoimmune diseases.” Clinical reviews in allergy & immunology
42.1 (2012): 71–8.
http://www.researchgate.net/publication/51823457_Leaky_gut_and_autoimmune_diseases
• Ghosh, Subrata et al. “New tools and approaches for improved management of inflammatory
bowel diseases.” Journal of Crohn’s and Colitis 8.10 (2014): 1246–53.
http://www.researchgate.net/publication/261756210_New_tools_and_approaches_for_improv
ed_management_of_inflammatory_bowel_diseases

• Kostic, Aleksandar, Ramnik Xavier, and Dirk Gevers. “The Microbiome in Inflammatory Bowel
Disease: Current Status and the Future Ahead.” Gastroenterology 146.6 (2014): 1489–99.
http://www.researchgate.net/publication/260374207_The_Microbiome_in_Inflammatory_Bow
el_Diseases_Current_Status_and_the_Future_Ahead
• Strober, Warren. “Impact of the gut microbiome on mucosal inflammation.” Trends in
Immunology (2013).
http://www.researchgate.net/publication/255984931_Impact_of_the_gut_microbiome_on_mu
cosal_inflammation
• Wlodarska, Marta, Aleksandar Kostic, and Ramnik Xavier. “An Integrative View of Microbiome-
Host Interactions in Inflammatory Bowel Diseases.” Cell Host & Microbe (2015).
http://www.researchgate.net/publication/276359033_An_Integrative_View_of_Microbiome-
Host_Interactions_in_Inflammatory_Bowel_Diseases

• Zippi, Maddalena. “Extraintestinal manifestations in a large series of Italian inflammatory
bowel disease patients.” World Journal of Gastroenterology 20.46 (2014): 17463-17467.
http://docrchive.com/document/extraintestinal-manifestations-in-a-large-series-of-italian-
inflammatory-bowel-disease-patients-7348008145211277/

The Microbiome Lifeline: Health Starts in the Mouth
• Atanasova, Kalina, and Özlem Yilmaz. “Prelude to oral microbes and chronic diseases: past,
present and future.” Microbes and Infection (2015).
http://www.researchgate.net/publication/274258034_Prelude_to_Oral_Microbes_and_Chronic
_Diseases_Past_Present_and_Future
• Costalonga, Massimo, and Mark Herzberg. “The oral microbiome and the immunobiology of
periodontal disease and caries.” Immunology Letters (2014).
http://www.researchgate.net/publication/268079979_The_oral_microbiome_and_the_immun
obiology_of_periodontal_disease_and_caries
• He, Jinzhi et al. “The oral microbiome diversity and its relation to human diseases.” Folia
Microbiologica (2014).
http://www.researchgate.net/publication/264987867_The_oral_microbiome_diversity_and_its
_relation_to_human_diseases

• Marsh, P, and D Bradshaw. “Dental plaque as a biofilm.” Journal of Industrial Microbiology
15.3 (1995): 169–175.
http://www.researchgate.net/publication/14678794_Dental_plaque_as_a_biofilm._J_Ind_
Microbiol
• Schwarzberg, Karen et al. “The Personal Human Oral Microbiome Obscures the Effects of
Treatment on Periodontal Disease.” PLoS ONE 9.1 (2014).
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086708
• Steinberg, Doron. “Dental Chatter: Bacterial Cross‐Talk in the Biofilm of the Oral Cavity.”
Israel Journal of Chemistry (2015).
http://onlinelibrary.wiley.com/doi/10.1002/ijch.201400143/abstract

• Struzycka, Izabela. “The oral microbiome in dental caries.” Polish journal of microbiology /
Polskie Towarzystwo Mikrobiologów = The Polish Society of Microbiologists 63.2 (2014):
127–35. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086708
• Warinner, Christina, Camilla Speller, and Matthew Collins. “A new era in
palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the
human oral microbiome.” Philosophical Transactions of the Royal Society of London B:
Biological Sciences 370.1660 (2015). http://www.pubfacts.com/detail/25487328/A-new-
era-in-palaeomicrobiology:-prospects-for-ancient-dental-calculus-as-a-long-term-record-of-
the-

• Zarco, Vess, and Ginsburg. “The oral microbiome in health and disease and the potential
impact on personalized dental medicine.” Oral Diseases 18.2 (2012): 109–120.
http://www.researchgate.net/publication/51628583_The_oral_microbiome_in_health_and
_disease_and_the_potential_impact_on_personalized_dental_medicine
• Zhang, Xuan et al. “The oral and gut microbiomes are perturbed in rheumatoid arthritis and
partly normalized after treatment.” Nature Medicine (2015).
http://www.researchgate.net/publication/280036160_The_oral_and_gut_microbiomes_ar
e_perturbed_in_rheumatoid_arthritis_and_partly_normalized_after_treatment

Data as an Enabling Tool:
Getting Closer to Precision Medicine

Big Data: Top-Down Bottom-Up Convergence
• Dove, Edward, Vural Özdemir, and Yann Joly. “Harnessing Omics Sciences, Population Databases, and
Open Innovation Models for Theranostics‐Guided Drug Discovery and Development.” Drug
Development Research (2012).
http://www.researchgate.net/publication/263060822_Harnessing_Omics_Sciences_Population_Dat
abases_and_Open_Innovation_Models_for_TheranosticsGuided_Drug_Discovery_and_Developmen
t
• Farh, Kyle et al. “Genetic and epigenetic fine mapping of causal autoimmune disease variants.”
Nature 518.7539 (2015): 337–43.
http://www.researchgate.net/publication/267753091_Genetic_and_epigenetic_fine_mapping_of_c
ausal_autoimmune_disease_variants
• Greene, Casey et al. “Understanding multicellular function and disease with human tissue-specific
networks.” Nature Genetics (2015).
http://www.researchgate.net/publication/275525447_Understanding_multicellular_function_and_d
isease_with_human_tissue-specific_networks

Rare Disease.” The American Journal of Human Genetics (2015).
http://www.researchgate.net/publication/279631558_The_Human_Phenotype_Ontology_Sem
antic_Unification_of_Common_and_Rare_Disease
• Ramos-Casals, Manuel et al. “Google-driven search for big data in autoimmune
geoepidemiology: Analysis of 394,827 patients with systemic autoimmune diseases.”
Autoimmunity Reviews (2015). http://www.researchgate.net/publication/274513423_Google-
driven_search_for_big_data_in_autoimmune_geoepidemiology_Analysis_of_394827_patients_
with_systemic_autoimmune_diseases

• Stanberry, Larissa et al. “Integrative Analysis of Longitudinal Metabolomics Data from a
Personal Multi-Omics Profile.” Metabolites (2013).
http://www.researchgate.net/publication/256413714_Integrative_Analysis_of_Longitudinal
_Metabolomics_Data_from_a_Personal_Multi-Omics_Profile
• Xu et al. “Comprehensive serological profiling of human populations using a synthetic
human virome.” Science (2015).
http://www.researchgate.net/publication/277778734_Viral_immunology._Comprehensive_
serological_profiling_of_human_populations_using_a_synthetic_human_virome

Systems Biology and Personal Data
• Kim, Ho-Youn, Hae-Rim Kim, and Sang-Heon Lee. “Advances in Systems Biology Approaches
for Autoimmune Diseases.” Immune Network 14.2 (2014): 73–80.
http://www.pubfacts.com/detail/24851096/Advances-in-systems-biology-approaches-for-
autoimmune-diseases
• Leung, Elaine et al. “Network-based drug discovery by integrating systems biology and
computational technologies.” Briefings in Bioinformatics 14.4 (2013): 491–505.
http://www.researchgate.net/publication/230644421_Network-
based_drug_discovery_by_integrating_systems_biology_and_computational_technologies
• Schork, and Nicholas. “Personalized medicine: Time for one-person trials.” Nature News
(2015).
http://www.researchgate.net/publication/275668184_Personalized_medicine_Time_for_o
ne-person_trials

Systems Biology and Personal Data
• Smarr, Larry. “Quantifying your body: A how‐to guide from a systems biology perspective.”
Biotechnology Journal 7.8 (2012): 980–991.
http://www.researchgate.net/publication/230658785_Quantifying_your_body_A_how-
to_guide_from_a_systems_biology_perspective

Predictive Modeling
• Ahmed, Usman et al. “Biomarkers of early stage osteoarthritis, rheumatoid arthritis and
musculoskeletal health.” Scientific Reports (2015).
http://www.researchgate.net/publication/273781983_Biomarkers_of_early_stage_osteoart
hritis_rheumatoid_arthritis_and_musculoskeletal_health
• Chopra, Monika, Kulwinder Singh, and Neelam Verma. “AUTOIMMUNE AND
INFLAMMATORY DISEASES BIOMARKERS.” International Journal of Biomedical and Advance
Research (2012).
http://www.researchgate.net/publication/272761554_AUTOIMMUNE_AND_INFLAMMATO
RY_DISEASES_BIOMARKERS

Predictive Modeling
• Dagan, Amir, and Shaye Kivity. "Cutting edge data in autoimmunity: as presented in the 9th
international congress of autoimmunity." Cutting Edge in Autoimmunity 61.1 (2015): 1-3.
Web
http://www.researchgate.net/publication/269177309_Cutting_edge_data_in_autoimmunit
y_as_presented_in_the_9th_international_congress_of_autoimmunity
• Jaberi‐Douraki, Majid et al. “Autoimmune responses in T1DM: quantitative methods to
understand onset, progression, and prevention of disease.” Pediatric Diabetes 15.3 (2014):
162–174.
http://www.researchgate.net/publication/262339657_Autoimmune_responses_in_T1DM_
quantitative_methods_to_understand_onset_progression_and_prevention_of_disease

Predictive Modeling
• Lee, James, and Kenneth Smith. “Prognosis in autoimmune and infectious disease: new insights
from genetics.” Clinical & Translational Immunology 3.5 (2014): 15.
http://www.researchgate.net/publication/269715667_Prognosis_in_autoimmune_and_infectio
us_disease_new_insights_from_genetics
• Norman, Jason et al. “Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel
Disease.” Cell (2015). http://www.researchgate.net/publication/271448551_Disease-
Specific_Alterations_in_the_Enteric_Virome_in_Inflammatory_Bowel_Disease
• Stanberry, Larissa et al. “Integrative Analysis of Longitudinal Metabolomics Data from a Personal
Multi-Omics Profile.” Metabolites (2013).
http://www.researchgate.net/publication/256413714_Integrative_Analysis_of_Longitudinal_M
etabolomics_Data_from_a_Personal_Multi-Omics_Profile
•

Autoimmunity:
Sorting through the Multiple Causes

Causes of Autoimmunity: Genetics & Genomics
• Archer, Nassif, and O’Brien. “Genetic variants of SLC11A1 are associated with both
autoimmune and infectious diseases: systematic review and meta-analysis.” Genes and
Immunity (2015).
http://www.researchgate.net/publication/274724921_Genetic_variants_of_SLC11A1_are_ass
ociated_with_both_autoimmune_and_infectious_diseases_systematic_review_and_meta-
analysis
• Dieli-Crimi, Romina, Carmen Cénit, and Concepción Núñez. “The genetics of celiac disease: A
comprehensive review of clinical implications.” Journal of Autoimmunity (2015).
http://www.mdlinx.com/allergy-immunology/medical-news-article/2015/07/21/celiac-
disease-epigenetics-gene-expression-hla/6248457/
• Farh, Kyle et al. “Genetic and epigenetic fine mapping of causal autoimmune disease
variants.” Nature 518.7539 (2015): 337–43.
http://www.nature.com/nature/journal/v518/n7539/full/nature13835.html

• Gupta, Bhawna, and David Hawkins. “Epigenomics of autoimmune diseases.” Immunology and
Cell Biology 93.3 (2015): 271–276.
http://www.nature.com/icb/journal/v93/n3/full/icb201518a.html
• Lee, James, and Kenneth Smith. “Prognosis in autoimmune and infectious disease: new insights
from genetics.” Clinical & Translational Immunology 3.5 (2014).
http://www.nature.com/cti/journal/v3/n5/full/cti20148a.html
• Marson, Alexander, William Housley, and David Hafler. “Genetic basis of autoimmunity.” Journal
of Clinical Investigation (2015). http://www.ncbi.nlm.nih.gov/pubmed/26030227
• McGarvey, Peter et al. “In silico analysis of autoimmune diseases and genetic relationships to
vaccination against infectious diseases.” BMC Immunology 15.1 (2014): 61.
http://www.researchgate.net/publication/267753091_Genetic_and_epigenetic_fine_mapping_
of_causal_autoimmune_disease_variants

• Mikacenic, Carmen et al. “Cutting edge: Genetic variation in TLR1 is associated with Pam3CSK4-
induced effector T cell resistance to regulatory T cell suppression.” Journal of immunology
(Baltimore, Md. : 1950) 193.12 (2014): 5786–90.
http://www.researchgate.net/publication/267931277_Cutting_Edge_Genetic_Variation_in_TLR
1_Is_Associated_with_Pam(3)CSK(4)-
Induced_Effector_T_Cell_Resistance_to_Regulatory_T_Cell_Suppression
• “NIH researchers reveal link between powerful gene regulatory elements and autoimmune
diseases.” National Institutes Into Health (2015).
http://www.nih.gov/news/health/feb2015/niams-17.htm
• Oftedal, Bergithe et al. “Dominant Mutations in the Autoimmune Regulator AIRE Are Associated
with Common Organ-Specific Autoimmune Diseases.” Immunity (2015).
http://www.researchgate.net/publication/278792204_Dominant_Mutations_in_the_Autoimmu
ne_Regulator_AIRE_Are_Associated_with_Common_Organ-Specific_Autoimmune_Diseases

• Parkes, Miles et al. “Genetic insights into common pathways and complex relationships
among immune-mediated diseases.” Nature Reviews Genetics (2013).
http://www.researchgate.net/publication/255689274_Genetic_insights_into_common_pat
hways_and_complex_relationships_among_immune-mediated_diseases._Nat_Rev_Genet
• Richardson, Bruce, and Dipak Patel. “Epigenetics in 2013: DNA methylation and miRNA—
key roles in systemic autoimmunity.” Nature Reviews Rheumatology 10.2 (2014): 72–74.
http://www.researchgate.net/publication/255689274_Genetic_insights_into_common_pat
hways_and_complex_relationships_among_immune-mediated_diseases._Nat_Rev_Genet

• Ritchie, Marylyn et al. “Methods of integrating data to uncover genotype-phenotype
interactions.” Nature Reviews Genetics (2015).
http://www.researchgate.net/publication/270910379_Methods_of_integrating_data_to_u
ncover_genotype-phenotype_interactions
• Wang, Xuefeng, Eric Xing, and Daniel Schaid. “Kernel methods for large-scale genomic data
analysis.” Briefings in bioinformatics 16.2 (2015): 183–92.
http://www.researchgate.net/publication/264164029_Kernel_methods_for_large-
scale_genomic_data_analysis
• Yang, Chin-An, and Bor-Luen Chiang. “Inflammasomes and human autoimmunity: A
comprehensive review.” Journal of Autoimmunity (2015).
http://www.researchgate.net/publication/49688650_Inflammasomes_and_autoimmunity

Causes of Autoimmunity: Environment
• Ballantyne, Sarah. The Paleo Approach. Las Vegas: Victory Belt Publishing Inc, 2013. Print.
• Blum, Susan. The Immune System Recovery Plan. New York: Scribner, 2013. Print.
• Bogdanos, Dimitrios et al. “Infectome: A platform to trace infectious triggers of
autoimmunity.” Autoimmunity Reviews 12.7 (2013): 726740.
http://www.researchgate.net/publication/233983999_Infectome_A_platform_to_trace_infec
tious_triggers_of_autoimmunity
• Campbell, Andrew. “Autoimmunity and the Gut.” Autoimmune Diseases 2014 (2014): 152428.
http://www.researchgate.net/publication/262886119_Autoimmunity_and_the_Gut
• Horton, Daniel et al. “Antibiotic Exposure and Juvenile Idiopathic Arthritis: A Case–Control
Study” Rutgers University (2015).
http://www.sciencedaily.com/releases/2015/07/150720092257.htm

• Javierre, Hernando, and Ballestar. “Environmental triggers and epigenetic deregulation in
autoimmune disease.” (2011).
http://www.researchgate.net/publication/51976993_Environmental_triggers_and_epigene
tic_deregulation_in_autoimmune_disease
Print.
• Obregon-Tito, Alexandra et al. “Subsistence strategies in traditional societies distinguish gut
microbiomes.” Nature Communications 6 (2015).
http://www.researchgate.net/publication/274071457_Subsistence_strategies_in_traditiona
l_societies_distinguish_gut_microbiomes

• Terato, Kuniaki, Christopher Do, and Hiroshi Shionoya. “Slipping through the Cracks: Linking Low
Immune Function and Intestinal Bacterial Imbalance to the Etiology of Rheumatoid Arthritis.”
Autoimmune Diseases 2015 (2015). http://www.hindawi.com/journals/ad/2015/636207/
• Velasquez-Manoff, Moises. An Epidemic of Absence. New York: Scribner, 2012. Print.
• Vojdani, Aristo. “A Potential Link between Environmental Triggers and Autoimmunity.”
Autoimmune Diseases 2014 (2014).
http://www.researchgate.net/publication/273894696_Slipping_through_the_Cracks_Linking_Low
_Immune_Function_and_Intestinal_Bacterial_Imbalance_to_the_Etiology_of_Rheumatoid_Arthri
tis
• Vojdani, Aristo, Michael Pollard, and Andrew Campbell. “Environmental Triggers and
Autoimmunity.” Autoimmune Diseases 2014 (2014): 798029.
http://www.researchgate.net/publication/271221861_Environmental_Triggers_and_Autoimmunit
y

Causes of Autoimmunity: Hormones
• Perlmutter, David. Grain Brain. New York: Little, Brown and Company, 2013. Print.

Causes of Autoimmunity: Pathogenesis
• Brady, David M. "Molecular Mimicry, the Hygiene Hypothesis, Stealth Infections and Other Examples
of Disconnect between Medical Research and the Practice of Clinical Medicine in Autoimmune
Disease" Open Journal of Rheumatology and Autoimmune Disease (2013): 33-39. Web.
http://www.researchgate.net/publication/262068728_Molecular_Mimicry_the_Hygiene_Hypothesis
_Stealth_Infections_and_Other_Examples_of_Disconnect_between_Medical_Research_and_the_Pr
actice_of_Clinical_Medicine_in_Autoimmune_Disease>
• Brusca, Abramson, and Scher. “Microbiome and mucosal inflammation as extra-articular triggers for
rheumatoid arthritis and autoimmunity.” (2014).
http://www.researchgate.net/publication/258700816_Brusca_S.B._Abramson_S.B.__Scher_J.U._Mic
robiome_and_mucosal_inflammation_as_extra-
articular_triggers_for_rheumatoid_arthritis_and_autoimmunity._Curr._Opin._Rheumatol._26_101-
107

• Craft, Joe, and Saeed Fatenejad. “Self antigens and epitope spreading in systemic
autoimmunity.” Arthritis & Rheumatism 40.8 (1997): 1374–1382.
http://onlinelibrary.wiley.com/doi/10.1002/art.1780400803/abstract
• Cusick, Libbey, and Fujinami. “Molecular mimicry as a mechanism of autoimmune disease”
(2012). http://www.ncbi.nlm.nih.gov/pubmed/22095454
• Farh, Kyle et al. “Genetic and epigenetic fine mapping of causal autoimmune disease variants.”
Nature 518.7539 (2015): 337–43.
http://www.nature.com/nature/journal/v518/n7539/full/nature13835.html#close
• McLean, Mairi et al. “Does the microbiota play a role in the pathogenesis of autoimmune
diseases?” Gut (2014).
http://www.researchgate.net/publication/268790142_Does_the_microbiota_play_a_role_in_th
e_pathogenesis_of_autoimmune_diseases

• Roederer, Mario et al. “The genetic architecture of the human immune system: a
bioresource for autoimmunity and disease pathogenesis.” Cell 161.2 (2015): 387–403.
http://www.cell.com/cell/abstract/S0092-8674(15)00247-0?rss=yes
• Rosenblum, Michael D., Kelly A. Remedios, and Abul K. Abbas. "Mechanisms of Human
Autoimmunity." The Journal of Clinical Investigation 125.6 (2015): 2228-2233. Web.
http://www.researchgate.net/publication/275217316_Mechanisms_of_human_autoimmu
nity
• Smilek, Dawn, and William Clair. “Solving the puzzle of autoimmunity: critical questions.”
F1000Prime Reports 7 (2015). http://www.ncbi.nlm.nih.gov/pubmed/25750735

• Theofilopoulos, Argyrios, Wolfgang Dummer, and Dwight Kono. “T cell homeostasis and
systemic autoimmunity.” Journal of Clinical Investigation 108.3 (2001): 335-340.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209358/
• Wen, Haitao, Edward Miao, and Jenny Ting. “Mechanisms of NOD-like Receptor-Associated
Inflammasome Activation.” Immunity 39.3 (2013).
http://www.sciencedirect.com/science/article/pii/S1074761313003890

Causes of Autoimmunity: Microbiome Diet
• Lerner, Aaron, and Torsten Matthias. “Changes in intestinal tight junction permeability
associated with industrial food additives explain the rising incidence of autoimmune
disease.” Autoimmunity Reviews (2015).
http://www.researchgate.net/publication/272186939_Changes_in_intestinal_tight_junctio
n_permeability_associated_with_industrial_food_additives_explain_the_rising_incidence_
of_autoimmune_disease
• Manzel, Arndt et al. “Role of ‘Western Diet’ in Inflammatory Autoimmune Diseases.”
Current Allergy and Asthma Reports 14.1 (2013): 404.
http://www.researchgate.net/publication/259335985_Role_of_Western_Diet_in_Inflamma
tory_Autoimmune_Diseases

Causes of Autoimmunity: Microbiome Diet
• Sonnenburg, Erica, and Justin Sonnenburg. “Starving our Microbial Self: The Deleterious
Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates.” Cell Metabolism
(2014).
http://www.researchgate.net/publication/265055722_Starving_our_Microbial_Self_The_D
eleterious_Consequences_of_a_Diet_Deficient_in_Microbiota-Accessible_Carbohydrates
• Youm, Yun-Hee et al. “The ketone metabolite β-hydroxybutyrate blocks NLRP3
inflammasome–mediated inflammatory disease.” Nature Medicine 21.3 (2015): 263–9.
http://www.researchgate.net/publication/272354552_The_ketone_metabolite_-
hydroxybutyrate_blocks_NLRP3_inflammasomemediated_inflammatory_disease

Prevention and Lifestyle Modifications
• “Translating the Science of Wellness and Healing.” Samueli Institute. 2011.
https://www.samueliinstitute.org/File%20Library/About%20Us/SP11_lowres.pdf

Prevention and Lifestyle Modifications: Food
• Ballantyne, Sarah. The Paleo Approach. Las Vegas: Victory Belt Publishing Inc, 2013. Print.
• Charlebois, Ashley, Greg Rosenfeld, and Brian Bressler. “The Impact of Dietary Interventions
on the Symptoms of Inflammatory Bowel Disease: A Systematic Review.” Critical Reviews in
Food Science and Nutrition (2015).
http://www.researchgate.net/publication/270651195_The_Impact_of_Dietary_Interventions
_on_the_Symptoms_of_Inflammatory_Bowel_Disease_A_Systematic_Review
• Clarke, and Mullin. “A Review of Complementary and Alternative Approaches to
Immunomodulation.” Nutrition in Clinical Practice 23.1 (2008): 49–62.
http://www.researchgate.net/publication/5647579_A_review_of_complementary_and_alter
native_approaches_to_immunomodulation

• Halmos, Emma, and Peter Gibson. “Dietary management of IBD—insights and advice.” Nature
Reviews Gastroenterology & Hepatology 12.3 (2015): 133–146.
http://www.researchgate.net/publication/272083767_Dietary_management_of_IBDinsights_a
nd_advice
• LeBlanc et al. “Bacteria as vitamin suppliers to their host: a gut microbiota perspective” (2013).
http://www.researchgate.net/publication/230782474_Bacteria_as_vitamin_suppliers_to_their
_host_A_gut_microbiota_perspective
• Mullin, Gerard and Kathie Swift. The Inside Tract. New York: Rodale, 2011. Print.
Print.

• Sanfilippo, Diane. Practical Paleo: a customized approach to health and a whole-foods
lifestyle. Las Vegas: Victory Belt Publishing Inc, 2012. Print.
• Subramanian, Sathish et al. “Cultivating Healthy Growth and Nutrition through the Gut
Microbiota.” Cell (2015).
http://www.researchgate.net/publication/274259147_Cultivating_Healthy_Growth_and_N
utrition_through_the_Gut_Microbiota

Prevention and Lifestyle Modifications: Exercise
• Brourman, Sherry, and Randy Rodman. Walk Yourself Well. www.SherryBrourman.com.
2005. Print.

Prevention and Lifestyle Modifications: Meditation
Print.

Prevention and Lifestyle Modifications: Digital Health
• Altshuler, David and et al. "Creating a Global Alliance to Enable Responsible Sharing of
Genomic and Clinical Data." 2013 June 3. http://genomicsandhealth.org/about-the-global-
alliance/key-documents/white-paper-creating-global-alliance-enable-responsible-shar
• Cnossen, Rick, Wendy Nilsen, et al. "White Paper: Data Collection and Mobile
Technologies." Precision Medicine Meeting (2014): 1-13 Web
http://www.nih.gov/precisionmedicine/whitepapers/Data-Collection-Mobile-
Technologies.pdf
• Elenko, Eric, Lindsay Underwood, and Daphne Zohar. “Defining digital medicine.” Nature
Biotechnology (2015).
http://www.researchgate.net/publication/276208474_Defining_digital_medicine

• Housman, Dan. "Marketing Research: Collaboration Proclamation." Medical Marketing &
Media (2015): 36- 37. Web. http://www.mmm-online.com/features/marketing-research-
collaboration-proclamation/article/400196/
• Maecker, Holden, Tamsin M. Lindstrom, and et al. "New Tools for Classification and
Monitoring of Autoimmune Diseases." Nature Reviews Rheumatology. 8.1 (2012): 317-328.
Web
http://www.researchgate.net/publication/225078353_New_tools_for_classification_and_
monitoring_of_autoimmune_diseases

• Margolis, Peter, Laura Peterson, and Michael Seid. “Collaborative Chronic Care Networks
(C3Ns) to transform chronic illness care.” Pediatrics 131.Supplement 4 (2013): S219–S223.
http://www.researchgate.net/publication/269912722_Collaborative_Chronic_Care_Networ
ks_(C3Ns)_to_Transform_Chronic_Illness_Care
• Milani, Richard, and Carl Lavie. “Health care 2020: reengineering health care delivery to
combat chronic disease.” The American journal of medicine 128.4 (2014): 337–43.
http://www.researchgate.net/publication/268692852_Health_Care_2020_Reengineering_
Health_Care_Delivery_to_Combat_Chronic_Disease
• Topol, Eric. The Patient Will See You Now. New York: Basic Books, 2015. Print.

Bridging the Autoimmune Abyss
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