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Showing 1 to 12 of 64 entries
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Characterization of candidate genes in inflammatory bowel disease-associated risk loci.

JCI insight

Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ.
PMID: 27668286
JCI Insight. 2016 Aug 18;1(13):e87899. doi: 10.1172/jci.insight.87899.

GWAS have linked SNPs to risk of inflammatory bowel disease (IBD), but a systematic characterization of disease-associated genes has been lacking. Prior studies utilized microarrays that did not capture many genes encoded within risk loci or defined expression quantitative...

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Peloquin JM, Goel G, Kong L, et al. Characterization of candidate genes in inflammatory bowel disease-associated risk loci. JCI Insight. 2016;1(13):e87899doi: 10.1172/jci.insight.87899.
Peloquin, J. M., Goel, G., Kong, L., Huang, H., Haritunians, T., Sartor, R. B., Daly, M. J., Newberry, R. D., McGovern, D. P., Yajnik, V., Lira, S. A., & Xavier, R. J. (2016). Characterization of candidate genes in inflammatory bowel disease-associated risk loci. JCI insight, 1(13), e87899. https://doi.org/10.1172/jci.insight.87899
Peloquin, Joanna M, et al. "Characterization of candidate genes in inflammatory bowel disease-associated risk loci." JCI insight vol. 1,13 (2016): e87899. doi: https://doi.org/10.1172/jci.insight.87899
Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ. Characterization of candidate genes in inflammatory bowel disease-associated risk loci. JCI Insight. 2016 Aug 18;1(13):e87899. doi: 10.1172/jci.insight.87899. PMID: 27668286; PMCID: PMC5033062.
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The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Cell host & microbe

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, Xavier RJ.
PMID: 25662751
Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 05.

Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the relationship between human gut microbiome dynamics throughout infancy and type 1 diabetes (T1D), we examined a cohort...

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Kostic AD, Gevers D, Siljander H, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260-73doi: 10.1016/j.chom.2015.01.001.
Kostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyötyläinen, T., Hämäläinen, A. M., Peet, A., Tillmann, V., Pöhö, P., Mattila, I., Lähdesmäki, H., Franzosa, E. A., Vaarala, O., de Goffau, M., Harmsen, H., Ilonen, J., Virtanen, S. M., Clish, C. B., Orešič, M., Huttenhower, C., Knip, M., & Xavier, R. J. (2015). The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell host & microbe, 17(2), 260-73. https://doi.org/10.1016/j.chom.2015.01.001
Kostic, Aleksandar D, et al. "The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes." Cell host & microbe vol. 17,2 (2015): 260-73. doi: https://doi.org/10.1016/j.chom.2015.01.001
Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, Xavier RJ. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 05. PMID: 25662751; PMCID: PMC4689191.
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For Application to Human Spaceflight and ISS Experiments: VESGEN Mapping of Microvascular Network Remodeling during Intestinal Inflammation.

Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology

Parsons-Wingerter P, Reinecker HC.
PMID: 25143705
Gravit Space Biol Bull. 2012 Oct 01;26(2):2-12.

Challenges to long-duration space exploration and colonization in microgravity and cosmic radiation environments by humans include poorly understood risks for gastrointestinal function and cancer. Nonetheless, constant remodeling of the intestinal microvasculature is critical for tissue viability, healthy wound healing,...

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Parsons-Wingerter P, Reinecker HC. For Application to Human Spaceflight and ISS Experiments: VESGEN Mapping of Microvascular Network Remodeling during Intestinal Inflammation. Gravit Space Biol Bull. 2012;26(2):2-12
Parsons-Wingerter, P., & Reinecker, H. C. (2012). For Application to Human Spaceflight and ISS Experiments: VESGEN Mapping of Microvascular Network Remodeling during Intestinal Inflammation. Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology, 26(2), 2-12.
Parsons-Wingerter, Patricia, and Reinecker, Hans-Christian. "For Application to Human Spaceflight and ISS Experiments: VESGEN Mapping of Microvascular Network Remodeling during Intestinal Inflammation." Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology vol. 26,2 (2012): 2-12.
Parsons-Wingerter P, Reinecker HC. For Application to Human Spaceflight and ISS Experiments: VESGEN Mapping of Microvascular Network Remodeling during Intestinal Inflammation. Gravit Space Biol Bull. 2012 Oct 01;26(2):2-12. PMID: 25143705; PMCID: PMC4136394.
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Bioinformatics for the Human Microbiome Project.

PLoS computational biology

Gevers D, Pop M, Schloss PD, Huttenhower C.
PMID: 23209389
PLoS Comput Biol. 2012;8(11):e1002779. doi: 10.1371/journal.pcbi.1002779. Epub 2012 Nov 29.

No abstract available.

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Gevers D, Pop M, Schloss PD, et al. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012;8(11):e1002779doi: 10.1371/journal.pcbi.1002779.
Gevers, D., Pop, M., Schloss, P. D., & Huttenhower, C. (2012). Bioinformatics for the Human Microbiome Project. PLoS computational biology, 8(11), e1002779. https://doi.org/10.1371/journal.pcbi.1002779
Gevers, Dirk, et al. "Bioinformatics for the Human Microbiome Project." PLoS computational biology vol. 8,11 (2012): e1002779. doi: https://doi.org/10.1371/journal.pcbi.1002779
Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 2012;8(11):e1002779. doi: 10.1371/journal.pcbi.1002779. Epub 2012 Nov 29. PMID: 23209389; PMCID: PMC3510052.
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AQP2 is necessary for vasopressin- and forskolin-mediated filamentous actin depolymerization in renal epithelial cells.

Biology open

Yui N, Lu HJ, Bouley R, Brown D.
PMID: 23213402
Biol Open. 2012 Feb 15;1(2):101-8. doi: 10.1242/bio.2011042. Epub 2011 Nov 04.

Remodeling of the actin cytoskeleton is required for vasopressin (VP)-induced aquaporin 2 (AQP2) trafficking. Here, we asked whether VP and forskolin (FK)-mediated F-actin depolymerization depends on AQP2 expression. Using various MDCK and LLC-PK1 cell lines with different AQP2 expression...

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Yui N, Lu HJ, Bouley R, et al. AQP2 is necessary for vasopressin- and forskolin-mediated filamentous actin depolymerization in renal epithelial cells. Biol Open. 2011;1(2):101-8doi: 10.1242/bio.2011042.
Yui, N., Lu, H. J., Bouley, R., & Brown, D. (2012). AQP2 is necessary for vasopressin- and forskolin-mediated filamentous actin depolymerization in renal epithelial cells. Biology open, 1(2), 101-8. https://doi.org/10.1242/bio.2011042
Yui, Naofumi, et al. "AQP2 is necessary for vasopressin- and forskolin-mediated filamentous actin depolymerization in renal epithelial cells." Biology open vol. 1,2 (2012): 101-8. doi: https://doi.org/10.1242/bio.2011042
Yui N, Lu HJ, Bouley R, Brown D. AQP2 is necessary for vasopressin- and forskolin-mediated filamentous actin depolymerization in renal epithelial cells. Biol Open. 2012 Feb 15;1(2):101-8. doi: 10.1242/bio.2011042. Epub 2011 Nov 04. PMID: 23213402; PMCID: PMC3507199.
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Functional profiling of the gut microbiome in disease-associated inflammation.

Genome medicine

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C.
PMID: 23906180
Genome Med. 2013 Jul 31;5(7):65. doi: 10.1186/gm469. eCollection 2013.

The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health and...

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Börnigen D, Morgan XC, Franzosa EA, et al. Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med. 2013;5(7):65doi: 10.1186/gm469.
Börnigen, D., Morgan, X. C., Franzosa, E. A., Ren, B., Xavier, R. J., Garrett, W. S., & Huttenhower, C. (2013). Functional profiling of the gut microbiome in disease-associated inflammation. Genome medicine, 5(7), 65. https://doi.org/10.1186/gm469
Börnigen, Daniela, et al. "Functional profiling of the gut microbiome in disease-associated inflammation." Genome medicine vol. 5,7 (2013): 65. doi: https://doi.org/10.1186/gm469
Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C. Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med. 2013 Jul 31;5(7):65. doi: 10.1186/gm469. eCollection 2013. PMID: 23906180; PMCID: PMC3978847.
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Intermittent hypoxia is a proinflammatory stimulus resulting in IL-6 expression and M1 macrophage polarization.

Hepatology communications

Schaefer E, Wu W, Mark C, Yang A, DiGiacomo E, Carlton-Smith C, Salloum S, Brisac C, Lin W, Corey KE, Chung RT.
PMID: 29404462
Hepatol Commun. 2017 May 18;1(4):326-337. doi: 10.1002/hep4.1045. eCollection 2017 Jun.

The biological factors that promote inflammation or nonalcoholic steatohepatitis (NASH) in the setting of nonalcoholic fatty liver disease remain incompletely understood. Clinical studies have demonstrated an association between obstructive sleep apnea (OSA) and both inflammation and fibrosis in NASH,...

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Schaefer E, Wu W, Mark C, et al. Intermittent hypoxia is a proinflammatory stimulus resulting in IL-6 expression and M1 macrophage polarization. Hepatol Commun. 2017;1(4):326-337doi: 10.1002/hep4.1045.
Schaefer, E., Wu, W., Mark, C., Yang, A., DiGiacomo, E., Carlton-Smith, C., Salloum, S., Brisac, C., Lin, W., Corey, K. E., & Chung, R. T. (2017). Intermittent hypoxia is a proinflammatory stimulus resulting in IL-6 expression and M1 macrophage polarization. Hepatology communications, 1(4), 326-337. https://doi.org/10.1002/hep4.1045
Schaefer, Esperance, et al. "Intermittent hypoxia is a proinflammatory stimulus resulting in IL-6 expression and M1 macrophage polarization." Hepatology communications vol. 1,4 (2017): 326-337. doi: https://doi.org/10.1002/hep4.1045
Schaefer E, Wu W, Mark C, Yang A, DiGiacomo E, Carlton-Smith C, Salloum S, Brisac C, Lin W, Corey KE, Chung RT. Intermittent hypoxia is a proinflammatory stimulus resulting in IL-6 expression and M1 macrophage polarization. Hepatol Commun. 2017 May 18;1(4):326-337. doi: 10.1002/hep4.1045. eCollection 2017 Jun. PMID: 29404462; PMCID: PMC5721395.
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Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis.

Genome biology

Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron L.
PMID: 30253799
Genome Biol. 2018 Sep 25;19(1):142. doi: 10.1186/s13059-018-1511-4.

BACKGROUND: Previous approaches to defining subtypes of colorectal carcinoma (CRC) and other cancers based on transcriptomes have assumed the existence of discrete subtypes. We analyze gene expression patterns of colorectal tumors from a large number of patients to test...

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Ma S, Ogino S, Parsana P, et al. Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018;19(1):142doi: 10.1186/s13059-018-1511-4.
Ma, S., Ogino, S., Parsana, P., Nishihara, R., Qian, Z., Shen, J., Mima, K., Masugi, Y., Cao, Y., Nowak, J. A., Shima, K., Hoshida, Y., Giovannucci, E. L., Gala, M. K., Chan, A. T., Fuchs, C. S., Parmigiani, G., Huttenhower, C., & Waldron, L. (2018). Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome biology, 19(1), 142. https://doi.org/10.1186/s13059-018-1511-4
Ma, Siyuan, et al. "Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis." Genome biology vol. 19,1 (2018): 142. doi: https://doi.org/10.1186/s13059-018-1511-4
Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron L. Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018 Sep 25;19(1):142. doi: 10.1186/s13059-018-1511-4. PMID: 30253799; PMCID: PMC6154428.
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Dietary Regulation of Adult Stem Cells.

Current stem cell reports

Mana MD, Kuo EY, Yilmaz ÖH.
PMID: 28966904
Curr Stem Cell Rep. 2017 Mar;3(1):1-8. doi: 10.1007/s40778-017-0072-x. Epub 2017 Feb 08.

PURPOSE OF REVIEW: Dietary intake is a critical regulator of organismal physiology and health. Tissue homeostasis and regeneration are dependent on adult tissue stem cells that self-renew and differentiate into the specialized cell types. As stem cells respond to...

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Mana MD, Kuo EY, Yilmaz ÖH. Dietary Regulation of Adult Stem Cells. Curr Stem Cell Rep. 2017;3(1):1-8doi: 10.1007/s40778-017-0072-x.
Mana, M. D., Kuo, E. Y., & Yilmaz, �. �. H. (2017). Dietary Regulation of Adult Stem Cells. Current stem cell reports, 3(1), 1-8. https://doi.org/10.1007/s40778-017-0072-x
Mana, Miyeko D, et al. "Dietary Regulation of Adult Stem Cells." Current stem cell reports vol. 3,1 (2017): 1-8. doi: https://doi.org/10.1007/s40778-017-0072-x
Mana MD, Kuo EY, Yilmaz ÖH. Dietary Regulation of Adult Stem Cells. Curr Stem Cell Rep. 2017 Mar;3(1):1-8. doi: 10.1007/s40778-017-0072-x. Epub 2017 Feb 08. PMID: 28966904; PMCID: PMC5614456.
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Asians have more perianal Crohn disease and ocular manifestations compared with white Americans.

Inflammatory intestinal diseases

Kochar B, Barnes EL, Herfarth HH, Martin CF, Ananthakrishnan AN, McGovern D, Long M, Sandler RS.
PMID: 29876356
Inflamm Intest Dis. 2018 Mar;2(3):147-153. doi: 10.1159/000484347. Epub 2017 Nov 18.

BACKGROUND: Inflammatory bowel disease (IBD) is increasing in Asians. We sought tobetter understand differences in IBD between Asians and whites in the United States (U.S.).METHODS: We used data from the Sinai-Helmsley Alliance for Research Excellence cohort to assess disease...

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Kochar B, Barnes EL, Herfarth HH, et al. Asians have more perianal Crohn disease and ocular manifestations compared with white Americans. Inflamm Intest Dis. 2017;2(3):147-153doi: 10.1159/000484347.
Kochar, B., Barnes, E. L., Herfarth, H. H., Martin, C. F., Ananthakrishnan, A. N., McGovern, D., Long, M., & Sandler, R. S. (2018). Asians have more perianal Crohn disease and ocular manifestations compared with white Americans. Inflammatory intestinal diseases, 2(3), 147-153. https://doi.org/10.1159/000484347
Kochar, Bharati, et al. "Asians have more perianal Crohn disease and ocular manifestations compared with white Americans." Inflammatory intestinal diseases vol. 2,3 (2018): 147-153. doi: https://doi.org/10.1159/000484347
Kochar B, Barnes EL, Herfarth HH, Martin CF, Ananthakrishnan AN, McGovern D, Long M, Sandler RS. Asians have more perianal Crohn disease and ocular manifestations compared with white Americans. Inflamm Intest Dis. 2018 Mar;2(3):147-153. doi: 10.1159/000484347. Epub 2017 Nov 18. PMID: 29876356; PMCID: PMC5986188.
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AAV-Mediated Gene Augmentation Therapy Restores Critical Functions in Mutant PRPF31.

Molecular therapy. Methods & clinical development

Brydon EM, Bronstein R, Buskin A, Lako M, Pierce EA, Fernandez-Godino R.
PMID: 31890732
Mol Ther Methods Clin Dev. 2019 Nov 11;15:392-402. doi: 10.1016/j.omtm.2019.10.014. eCollection 2019 Dec 13.

Retinitis pigmentosa (RP) is the most common form of inherited vision loss and is characterized by degeneration of retinal photoreceptor cells and the retinal pigment epithelium (RPE). Mutations in pre-mRNA processing factor 31 (

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Brydon EM, Bronstein R, Buskin A, et al. AAV-Mediated Gene Augmentation Therapy Restores Critical Functions in Mutant PRPF31. Mol Ther Methods Clin Dev. 2019;15:392-402doi: 10.1016/j.omtm.2019.10.014.
Brydon, E. M., Bronstein, R., Buskin, A., Lako, M., Pierce, E. A., & Fernandez-Godino, R. (2019). AAV-Mediated Gene Augmentation Therapy Restores Critical Functions in Mutant PRPF31. Molecular therapy. Methods & clinical development, 15392-402. https://doi.org/10.1016/j.omtm.2019.10.014
Brydon, Elizabeth M, et al. "AAV-Mediated Gene Augmentation Therapy Restores Critical Functions in Mutant PRPF31." Molecular therapy. Methods & clinical development vol. 15 (2019): 392-402. doi: https://doi.org/10.1016/j.omtm.2019.10.014
Brydon EM, Bronstein R, Buskin A, Lako M, Pierce EA, Fernandez-Godino R. AAV-Mediated Gene Augmentation Therapy Restores Critical Functions in Mutant PRPF31. Mol Ther Methods Clin Dev. 2019 Nov 11;15:392-402. doi: 10.1016/j.omtm.2019.10.014. eCollection 2019 Dec 13. PMID: 31890732; PMCID: PMC6909184.
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Translating the human microbiome: a path to improving health.

Genome medicine

Xavier RJ.
PMID: 33952319
Genome Med. 2021 May 05;13(1):78. doi: 10.1186/s13073-021-00896-w.

No abstract available.

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Xavier RJ. Translating the human microbiome: a path to improving health. Genome Med. 2021;13(1):78doi: 10.1186/s13073-021-00896-w.
Xavier, R. J. (2021). Translating the human microbiome: a path to improving health. Genome medicine, 13(1), 78. https://doi.org/10.1186/s13073-021-00896-w
Xavier, Ramnik J. "Translating the human microbiome: a path to improving health." Genome medicine vol. 13,1 (2021): 78. doi: https://doi.org/10.1186/s13073-021-00896-w
Xavier RJ. Translating the human microbiome: a path to improving health. Genome Med. 2021 May 05;13(1):78. doi: 10.1186/s13073-021-00896-w. PMID: 33952319; PMCID: PMC8097784.
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Showing 1 to 12 of 64 entries