Publications

Tae Sung Kim, Tomoko Ikeuch, Vasileios Ionas Theofilou, Teresa Greenwell-Wild, June Armond, Emanuel Adade*, Lu Li, Loreto Abusleme, Nicolas Dutzan, Drake Winslow Williams, Yao Yuan, Laurie Brenchley, NIDCD/NIDCR Genomics and Computational Biology Core, Robert J Palmer, Ramiro Iglesias-Bartolome, Giorgio Trinchieri, Stavros Garantziotis, Yasmine Belkaid, Alex M Valm, Patricia I Diaz, Steven M. Holland, Niki M. Moutsopoulos. Microbe sensing triggers epithelial IL-23 to promote oral mucosal immunopathology. Immunity 2024 Mar 19:S1074-7613(24)00096-7. doi: 10.1016/j.immuni.2024.02.020. PMID: 38513665

Lemus AA & Valm AM. In vitro dental plaque model for systems-level imaging and spatial analyses. 2023. Curr Prot Cell Biol. PMID: 37830790

Sarkar K, Kotb NM, Lemus A, Martin ET, McCarthy E, Camacho J, Iqbal A, Valm AM, Sammons MA, Rangan P. 2023. A feedback loop between heterochromatin and the nucleopore complex controls germ-cell to oocyte transition during Drosophila oogenesis. Dev Cell. 2023 Aug 28:S1534-5807(23)00412-4. doi: 10.1016/j.devcel.2023.08.014. Online ahead of print. PMID: 37673064

Wang R, Lemus AA, Henneberry CM, Ying Y, Feng Y, and Valm AM. Unmixing Biological Fluorescence Image Data with Sparse and Low-Rank Poisson Regression. Bioinformatics. 2023 Apr 3; 39(4):btad159. doi: 10.1093/bioinformatics/btad159 PMID: 36964716 %Co-corresponding authors

Adade EA*, Stevick RJ*, Pérez-Pascual D, Ghigo J-M%, Valm, AM%. Gnotobiotic zebrafish microbiota display inter-individual variability affecting host physiology. 2023. BioRχiv. *Co-first authors; %Co-corresponding authors

Adade EA*, Al Lakhen K*, Lemus AA*, Valm AM. Recent progress in analyzing the spatial structure of the human microbiome: Distinguishing biogeography and architecture in the oral and gut communities. 2021. Curr Opin Endocrine and Metabolic Res. 18: 275-283. doi: 10.1016/j.coemr.2021.04.005. PMID: *Contributed Equally

Krishnamoorthy AL, Lemus AA, Solomon AP, Valm AM, Neelakantan P. Enterococcus faecalis enhances Candida albicans mediated tissue destruction in a strain-dependent manner. 2020. Microorganisms. 8(11): 1771. doi: 10.3390/microorganisms8111771. PMID: 33187237

Diaz, PI & Valm, AM. Microbial interactions in dental plaque. 2019. J Dent Res. doi: 10.1177/0022034519880157. PMID: 31590609

Valm, AM. Oral microbial community structure in the transition from health to disease. 2019. J Mol Biol. 431(16):2957-2969. doi: 10.1016/j.jmb.2019.05.016

Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, Polley EC, Bowman ED, Khan MA, Robles AI, Cooks T, Ryan BM, Padgett N, Dzutsev AH, Trinchieri G, Pineda MA, Bilke S, Meltzer PS, Hokenstad AN, Stickrod TM, Walther-Antonio MR, Earl JP, Mell JC, Krol JE, Balashov SV, Bhat AS, Ehrlich GD, Valm A, Deming C, Conlan S, Oh J, Segre JA, Harris CC. Interaction between the microbiome and TP53 in human lung cancer. 2018. Genome Biol. 19(1): 123. doi: 10.1186/s13059-018-1501-6

 S. Cohen, A.M. Valm, J. Lippincott-Schwartz. Interacting Organelles. 2018. Curr Opinion Cell Biol. 53: 84-91. doi: 10.1016/j.ceb.2018.06.003

 S. Cohen, A.M. Valm, J. Lippincott-Schwartz. Multispectral Live-Cell Imaging. 2018. Curr Protocols in Cell Biol  79(1): e46. doi: 10.1002/cpcb.46

Stefan CJ, Trimble WS, Grinstein S, Drin G, Reinisch K, De Camilli P, Cohen S, Valm AM, Lippincott-Schwartz J, Levine TP, Iaea DB, Maxfield FR, Futter CE, Eden ER, Judith D, van Vliet AR, Agostinis P, Tooze SA, Sugiura A, McBride HM. Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers. 2017. BMC Biol. 15: 102. doi: 10.1186/s12915-017-0432-0. PMID: 29089042.

Valm AM, S. Cohen, W. Legant, J. Melunis, U. Hershberg, E. Wait, A.R. Cohen, M. Davidson, E. Betzig, J. Lippincott-Schwartz.   Applying systems-level spectral imaging and analysis to reveal the organelle interactome. 2017.Nature 546:162-167. doi: 10.1038/nature22369. PMID: 28538724.

Palmer, Jr. RJ, Shah N, Valm A, Paster B, Dewhirst F, Inue T, Cisar JO. Complementary molecular and phenotypic characterization of an oral bacterial biofilm community in two individuals. 2017. Applied Environ. Microbiol. 83(11). pii:e00407-17. doi: 10.1128/AEM.00407-17. PMID: 28341674.

Valm AM, Oldenbourg R, Borisy GG. Multiplexed spectral imaging of 120 different fluorescent labels. 2016. PLoS One 11(7):e0158495. doi: 10.1371/journal.pone.0158495. PMID: 27391327.

Valm AM, Mark Welch JL, Oldenbourg R, and Borisy GG. CLASI-FISH: Principles of Combinatorial Labeling and Spectral Imaging for greatly expanding the number of distinguishable microbes in a single image.  2011. Syst. Appl. Microbiol. 35(8):496-502. doi: 10.1016/j.syapm.2012.03.004. PMID: 22521573.

Valm AM, Mark Welch J, Rieken CW, Hasegawa Y, Sogin ML, Oldenbourg R, Dewhirst FE, Borisy GG. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. 2011. Proc Natl Acad Sci USA 108(10):4152-7. doi: 10.1073/pnas.1101134108. PMID: 21325608.

Hasegawa Y, Mark Welch J, Valm AM, Rieken CW, Sogin ML, Borisy GG. Imaging marine bacteria with unique 16S rRNA V6 sequences by fluorescence in situ hybridization and spectral analysis. 2010. Geomicrobiology J. 27(3):251-260. doi: dx.doi.org/10.1080/01490450903456806.