Publications

B Man, M Koenig, B Bernabe, U Nagelli, L Tussing-Humphreys. The Role of the Gut Microbiota in the Prevention and Management of Gestational Diabetes Mellitus: Are We There Yet? The Journal of Perinatal & Neonatal Nursing 34 (3), 195-198

Alexander Zaborin, Beatriz Penalver Bernabe, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A Gilbert, Olga Zaborina, John C Alverdy. Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics  Msystems 5 (3)

A McLeod, B Bernabe, L Schiffer, M Fitzgibbon, L Tussing-Humphreys. Effect of a Mediterranean Diet Intervention with and Without Weight Loss on the Gut Microbiota in Obese, Older Adult Current Developments in Nutrition 4 (Supplement_2), 1575-1575

BP Bernabe, S Dowty, L Pezley, N Goel, E Hill, R Gibbons, L Tussing-Humphreys, P Maki, J Gilbert.  Depression During Pregnancy is Associated With an Altered Gut Microbiome in an Urban Diverse Population Biological Psychiatry 87 (9), S36

BP Bernabe, H Rackers, S Dowty, L Tussing-Humphreys, L Pezley, S Meltzer-Brody, R Knickmeyer, I Carroll, P Maki, J Gilbert, M Kimmel. Host Immunity, the Microbiome, and Perinatal Anxiety Biological Psychiatry 87 (9), S36-S37

BP Bernabé, PM Maki, SM Dowty, M Salas, L Cralle, Z Shah, JA Gilbert. Precision medicine in perinatal depression in light of the human microbiome Psychopharmacology, 1-27

BP Bernabé, T Woodruff, LJ Broadbelt, LD Shea. Ligands, Receptors, and Transcription Factors that Mediate Inter-Cellular and Intra-Cellular Communication during Ovarian Follicle Development Reproductive Sciences 27 (2), 690-703

Bernabé BP, Tussing-Humphreys L, Rackers HS, Welke L, Mantha A, Kimmel MC. Improving Mental Health for the Mother-Infant Dyad by Nutrition and the Maternal Gut Microbiome. Gastroenterol Clin North Am. 2019 Sep;48(3):433-445. doi: 10.1016/j.gtc.2019.04.007. Review. PubMed PMID: 31383280.

Fei N, Bernabé BP, Lie L, Baghdan D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Gottel N, Riesen W, Korte W, Luke A, Kliethermes SA, Layden BT, Gilbert JA, Dugas LR. The human microbiota is associated with cardiometabolic risk across the epidemiologic transition. PLoS One. 2019;14(7):e0215262. doi: 10.1371/journal.pone.0215262. eCollection 2019. PubMed PMID: 31339887; PubMed Central PMCID: PMC6656343.

Peñalver Bernabé B, Thiele I, Galdones E, Siletz A, Chandrasekaran S, Woodruff TK, Broadbelt LJ, Shea LD. Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. BMC Bioinformatics. 2019 Jun 10;20(1):307. doi: 10.1186/s12859-019-2825-2. PubMed PMID: 31182013; PubMed Central PMCID: PMC6558917.

B Penalver Bernabe, S Dowty, L Pezley, Z Shah, N Goel, E Hill, R Gibbons, L Tussing-Humphreys, P Maki, J Gilbert. S87. Depression During Pregnancy is Associated With an Altered Gut Microbiome. Biological Psychiatry 85 (10), S330. DOI: https://doi.org/10.1016/j.biopsych.2019.03.838

BP Bernabe, JA Gilbert. Dynamic Core Taxonomical and Metabolic Signatures in the Perinatal Period. REPRODUCTIVE SCIENCES, 2019

Peñalver Bernabé B, Cralle L, Gilbert JA. Systems biology of the human microbiome. Curr Opin Biotechnol. 2018 Jun;51:146-153. doi: 10.1016/j.copbio.2018.01.018. Epub 2018 Feb 14. Review. PubMed PMID: 29453029.

Peñalver Bernabé B, Shin S, Rios PD, Broadbelt LJ, Shea LD, Seidlits SK. Dynamic transcription factor activity networks in response to independently altered mechanical and adhesive microenvironmental cues. Integr Biol (Camb). 2016 Aug 8;8(8):844-60. doi: 10.1039/c6ib00093b. Epub 2016 Jul 29. PubMed PMID: 27470442; PubMed Central PMCID: PMC4981188.

Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD. Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy. Integr Biol (Camb). 2014 Dec;6(12):1170-82. doi: 10.1039/c4ib00086b. PubMed PMID: 25303361; PubMed Central PMCID: PMC4237672.

Tagler D, Makanji Y, Tu T, Bernabé BP, Lee R, Zhu J, Kniazeva E, Hornick JE, Woodruff TK, Shea LD. Promoting extracellular matrix remodeling via ascorbic acid enhances the survival of primary ovarian follicles encapsulated in alginate hydrogels. Biotechnol Bioeng. 2014 Jul;111(7):1417-29. doi: 10.1002/bit.25181. Epub 2014 Jan 22. PubMed PMID: 24375265; PubMed Central PMCID: PMC4232184.

Tarasewicz E, Rivas L, Hamdan R, Dokic D, Parimi V, Bernabe BP, Thomas A, Shea LD, Jeruss JS. Inhibition of CDK-mediated phosphorylation of Smad3 results in decreased oncogenesis in triple negative breast cancer cells. Cell Cycle. 2014;13(20):3191-201. doi: 10.4161/15384101.2014.950126. PubMed PMID: 25485498; PubMed Central PMCID: PMC4614520.

Skory RM, Bernabé BP, Galdones E, Broadbelt LJ, Shea LD, Woodruff TK. Microarray analysis identifies COMP as the most differentially regulated transcript throughout in vitro follicle growth. Mol Reprod Dev. 2013 Feb;80(2):132-44. doi: 10.1002/mrd.22144. Epub 2013 Jan 30. PubMed PMID: 23242557; PubMed Central PMCID: PMC3730266.

Bellis AD, Bernabé BP, Weiss MS, Shin S, Weng S, Broadbelt LJ, Shea LD. Dynamic transcription factor activity profiling in 2D and 3D cell cultures. Biotechnol Bioeng. 2013 Feb;110(2):563-72. doi: 10.1002/bit.24718. Epub 2012 Sep 18. PubMed PMID: 22949103; PubMed Central PMCID: PMC4073638.

Mutharasan P, Galdones E, Peñalver Bernabé B, Garcia OA, Jafari N, Shea LD, Woodruff TK, Legro RS, Dunaif A, Urbanek M. Evidence for chromosome 2p16.3 polycystic ovary syndrome susceptibility locus in affected women of European ancestry. J Clin Endocrinol Metab. 2013 Jan;98(1):E185-90. doi: 10.1210/jc.2012-2471. Epub 2012 Nov 1. PubMed PMID: 23118426; PubMed Central PMCID: PMC3537106.

MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J. State-time spectrum of signal transduction logic models. Phys Biol. 2012 Aug;9(4):045003. doi: 10.1088/1478-3975/9/4/045003. Epub 2012 Aug 7. Review. PubMed PMID: 22871648.

Weiss MS, Bernabé BP, Shikanov A, Bluver DA, Mui MD, Shin S, Broadbelt LJ, Shea LD. The impact of adhesion peptides within hydrogels on the phenotype and signaling of normal and cancerous mammary epithelial cells. Biomaterials. 2012 May;33(13):3548-59. doi: 10.1016/j.biomaterials.2012.01.055. Epub 2012 Feb 15. PubMed PMID: 22341213; PubMed Central PMCID: PMC3288720.

Mutharasan P, Galdones E, Peñalver Bernabé B, Garcia OA, Jafari N, Shea LD, Woodruff TK, Legro RS, Dunaif A, Urbanek M. Evidence for chromosome 2p16.3 polycystic ovary syndrome susceptibility locus in affected women of European ancestry. J Clin Endocrinol Metab. 2013 Jan;98(1):E185-90. doi: 10.1210/jc.2012-2471. Epub 2012 Nov 1. PubMed PMID: 23118426; PubMed Central PMCID: PMC3537106.

Bellis AD, Bernabé BP, Weiss MS, Shin S, Weng S, Broadbelt LJ, Shea LD. Dynamic transcription factor activity profiling in 2D and 3D cell cultures. Biotechnol Bioeng. 2013 Feb;110(2):563-72. doi: 10.1002/bit.24718. Epub 2012 Sep 18. PubMed PMID: 22949103; PubMed Central PMCID: PMC4073638.

Bellis AD, Peňalver-Bernabé B, Weiss MS, Yarrington ME, Barbolina MV, Pannier AK, Jeruss JS, Broadbelt LJ, Shea LD. Cellular arrays for large-scale analysis of transcription factor activity. Biotechnol Bioeng. 2011 Feb;108(2):395-403. doi: 10.1002/bit.22916. PubMed PMID: 20812256; PubMed Central PMCID: PMC3022829.

Weiss MS, Peñalver Bernabé B, Bellis AD, Broadbelt LJ, Jeruss JS, Shea LD. Dynamic, large-scale profiling of transcription factor activity from live cells in 3D culture. PLoS One. 2010 Nov 17;5(11):e14026. doi: 10.1371/journal.pone.0014026. PubMed PMID: 21103341; PubMed Central PMCID: PMC2984444.