Graduate School of Biomedical Sciences

Initiative for Maximizing Student Development Publications


Successful IMSD students publish one or more research articles upon graduation.


2023/2024 Publications


Si H, Esquivel M, Mendoza Mendoza E, Roarty K. The covert symphony: cellular and molecular accomplices in breast cancer metastasis. Front Cell Dev Biol. 2023 Jun 27;11:1221784. doi: 10.3389/fcell.2023.1221784. PMID: 37440925; PMCID: PMC10333702.

van der Heijden ME, Rey Hipolito AG, Kim LH, Kizek DJ, Perez RM, Lin T, Sillitoe RV. Glutamatergic cerebellar neurons differentially contribute to the acquisition of motor and social behaviors. Nat Commun. 2023 May 15;14(1):2771. doi: 10.1038/s41467-023-38475-9. PMID: 37188723; PMCID: PMC10185563.

Perez R, Park Y, Hirano A, Brecha N, Frankfort B, Zuniga-Sanchez E. Modeling subcellular specificity in the developing retina. Res Sq [Preprint]. 2023 Aug doi: 10.21203/ PMID: 37609217; PMCID: PMC10441513.

Baek ML, Lee J, Pendleton KE, Berner MJ, Goff EB, Tan L, Martinez SA, Mahmud I, Wang T, Meyer MD, Lim B, Barrish JP, Porter W, Lorenzi PL, Echeverria GV. Mitochondrial structure and function adaptation in residual triple negative breast cancer cells surviving chemotherapy treatment. Oncogene. 2023 Mar;42(14):1117-1131. doi: 10.1038/s41388-023-02596-8. Epub 2023 Feb 22. PMID: 36813854; PMCID: PMC10069007.

Koller EJ, Comstock M, Bean JC, Escobedo G, Park KW, Jankowsky JL. Correction: Temporal and spatially controlled APP transgene expression using Cre-dependent alleles. Dis Model Mech. 2023 Mar 1;16(3): dmm050136. doi: 10.1242/dmm.050136. Epub 2023 Mar 8. Erratum for: Dis Model Mech. 2022 May 1;15(5): PMID: 36897116; PMCID: PMC10040240.

LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genom. 2023 Apr 20;3(5):100303. doi: 10.1016/j.xgen.2023.100303. PMID: 37228754; PMCID: PMC10203258.

Konecki DM, Hamrick S, Wang C, Agosto MA, Wensel TG, Lichtarge O. CovET: A covariation-evolutionary trace method that identifies protein structure-function modules. J Biol Chem. 2023 Jul;299(7):104896. doi: 10.1016/j.jbc.2023.104896. Epub 2023 Jun 7. PMID: 37290531; PMCID: PMC10338321.

Rey Hipolito AG, van der Heijden ME, Sillitoe RV. Physiology of Dystonia: Animal Studies. Int Rev Neurobiol. 2023; 169:163-215. doi: 10.1016/bs.irn.2023.05.004. Epub 2023 May 17. PMID: 37482392.

Brown AM, Lackey EP, Salazar Leon LE, Rey Hipolito AG, Beckinghausen J, Lin T, Sillitoe RV. Electromyography as a Method for Distinguishing Dystonia in Mice. Adv Neurobiol. 2023; 31:71-91. doi: 10.1007/978-3-031-26220-3_5. PMID: 37338697.

Hao X, Shen Y, Chen N, Zhang W, Valverde E, Wu L, Chan HL, Xu Z, Yu L, Gao Y, Bado I, Michie LN, Rivas CH, Dominguez LB, Aguirre S, Pingel BC, Wu YH, Liu F, Ding Y, Edwards DG, Liu J, Alexander A, Ueno NT, Hsueh PR, Tu CY, Liu LC, Chen SH, Hung MC, Lim B, Zhang XH. Osteoprogenitor-GMP crosstalk underpins solid tumor-induced systemic immunosuppression and persists after tumor removal. Cell Stem Cell. 2023 May 4;30(5):648-664.e8. doi: 10.1016/j.stem.2023.04.005. PMID: 37146584; PMCID: PMC10165729.

Adeniyi-Ipadeola G, Nwanosike H, Ramani S. Human intestinal organoids as models to study enteric bacteria and viruses. Curr Opin Microbiol. 2023 Oct; 75: 102362. doi: 10.1016/j.mib. 2023.102362. Epub 2023 Aug 1. PMID: 37536261.

Adeniyi-Ipadeola GO, Hankins JD, Kambal A, Zeng XL, Patil K, Poplaski V, Bomidi C, Nguyen-Phuc H, Grimm SL, Coarfa C, Crawford SE, Blutt SE, Speer AL, Estes MK, Ramani S. Infant and Adult Human Intestinal Enteroids are Morphologically and Functionally Distinct. bioRxiv [Preprint]. 2023 May 20:2023.05.19.541350. doi: 10.1101/2023.05.19.541350. PMID: 37292968; PMCID: PMC10245709.

Emig AA, Williams MLK. Gastrulation morphogenesis in synthetic systems. Semin Cell Dev Biol. 2023 May 30; 141: 3-13. doi: 10.1016/j.semcdb. 2022.07.002. Epub 2022 Jul 9. PMID: 35817656; PMCID: PMC9825685.

Cooke MB, Herman C. Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex. J Bacteriol. 2023 Mar 21;205(3): e0043822. doi: 10.1128/jb.00438-22. Epub 2023 Feb 27. PMID: 36847532; PMCID: PMC10029717.

Zhang F, Blackburn D, Hosea CN, Assié A, Samuel BS. Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome. J Vis Exp. 2023 Mar 31;(193). doi: 10.3791/64605. PMID: 37067276.

Whidbey C, Konopaski AN, Teshome R, Dhaliwal S, Peters MQ, Mejia ME, Ballard MB, Patras KA. Complete Genome Sequences of 37 Bacteria from the Human Vaginal Tract. Microbiol Resour Announc. 2023 Jun 20;12(6): e0035823. doi: 10.1128/mra.00358-23. Epub 2023 May 23. PMID: 37219419; PMCID: PMC10281102.

Mejia ME, Robertson CM, Patras KA. Interspecies Interactions within the Host:
the Social Network of Group B <i>Streptococcus</i>. Infect Immun. 2023 Apr
18;91(4): e0044022. doi: 10.1128/iai.00440-22. Epub 2023 Mar 28. PMID: 36975791; PMCID: PMC10112235.

Caldwell C, Salihu HM, Dongarwar D, Mercado-Evans V, Batiste A, Beal T, Valladares E. Breastfeeding Practices of Women with HIV in Sub-Saharan Africa. Nurs Womens Health. 2023 Aug 11: S1751-4851(23)00145-9. doi: 10.1016/j.nwh.2023.03.006. Epub ahead of print. PMID: 37579921.

Jain K, Marunde MR, Burg JM, Gloor SL, Joseph FM, Poncha KF, Gillespie ZB, Rodriguez KL, Popova IK, Hall NW, Vaidya A, Howard SA, Taylor HF, Mukhsinova L, Onuoha UC, Patteson EF, Cooke SW, Taylor BC, Weinzapfel EN, Cheek MA, Meiners MJ, Fox GC, Namitz KEW, Cowles MW, Krajewski K, Sun ZW, Cosgrove MS, Young NL, Keogh MC, Strahl BD. An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability. Elife. 2023 May 19; 12: e82596. doi: 10.7554/eLife.82596. PMID: 37204295; PMCID: PMC10229121.

Masschelin PM, Saha P, Ochsner SA, Cox AR, Kim KH, Felix JB, Sharp R, Li X, Tan L, Park JH, Wang L, Putluri V, Lorenzi PL, Nuotio-Antar AM, Sun Z, Kaipparettu BA, Putluri N, Moore DD, Summers SA, McKenna NJ, Hartig SM. Vitamin B2 enables regulation of fasting glucose availability. Elife. 2023 Jul 7; 12: e84077. doi: 10.7554/eLife.84077. PMID: 37417957; PMCID: PMC10328530.

Le DT, Florez MA, Kus P, Tran BT, Kain B, Zhu Y, Christensen K, Jain A, Malovannaya A, King KY. BATF2 promotes HSC myeloid differentiation by amplifying IFN response mediators during chronic infection. iScience. 2023 Jan 27;26(2):106059. doi: 10.1016/j.isci.2023.106059. PMID: 36824275; PMCID: PMC9942003.

Kain BN, Tran BT, Luna PN, Cao R, Le DT, Florez MA, Maneix L, Toups JD, Morales-Mantilla DE, Koh S, Han H, Jaksik R, Huang Y, Catic A, Shaw CA, King KY. Hematopoietic stem and progenitor cells confer cross-protective trained immunity in mouse models. iScience. 2023 Aug 9; 26 (9): 107596. doi: 10.1016/j.isci.2023.107596. PMID: 37664586; PMCID: PMC10470378.

Lewis MA, Cortés-Penfield NW, Ettayebi K, Patil K, Kaur G, Neill FH, Atmar RL, Ramani S, Estes MK. A Standardized Antiviral Pipeline for Human Norovirus in Human Intestinal Enteroids Demonstrates No Antiviral Activity of Nitazoxanide. bioRxiv [Preprint]. 2023 May 23: 2023.05.23.542011. doi: 10.1101/2023.05.23.542011. PMID: 37293103; PMCID: PMC10245936.

Pierzchlewicz PA, Willeke KF, Nix AF, Elumalai P, Restivo K, Shinn T, Nealley C, Rodriguez G, Patel S, Franke K, Tolias AS, Sinz FH. Energy Guided Diffusion for Generating Neurally Exciting Images. bioRxiv [Preprint]. 2023 May 20:2023.05.18.541176. doi: 10.1101/2023.05.18.541176. PMID: 37292670; PMCID: PMC10245650.

Adewunmi O, Shen Y, Zhang XH, Rosen JM. Targeted inhibition of lncRNA Malat1 alters the tumor immune microenvironment in preclinical syngeneic mouse models of triple negative breast cancer. Cancer Immunol Res. 2023 Aug 21: CIR-23-0045. doi: 10.1158/2326-6066.CIR-23-0045. Epub ahead of print. PMID: 37603945.

Zhang W, Xu Z, Hao X, He T, Li J, Shen Y, Liu K, Gao Y, Liu J, Edwards DG, Muscarella AM, Wu L, Yu L, Xu L, Chen X, Wu YH, Bado IL, Ding Y, Aguirre S, Wang H, Gugala Z, Satcher RL, Wong STC, Zhang XH. Bone Metastasis Initiation Is Coupled with Bone Remodeling through Osteogenic Differentiation of NG2+ Cells. Cancer Discov. 2023 Feb 6;13(2):474-495. doi: 10.1158/2159-8290.CD-22-0220. PMID: 36287038; PMCID: PMC9905315.

Brandel-Ankrapp, Katie, Arey, Rachel - Uncovering novel regulators of memory using C. elegans genetic and genomic analysis - Biochem Soc Trans, 2023 Feb 27;51(1):161-171. doi: 10.1042/BST20220455.

Xing Y, Clark JR, Chang JD, Chirman DM, Green S, Zulk JJ, Jelinski J, Patras KA, Maresso AW. Broad protective vaccination against systemic Escherichia coli with autotransporter antigens. PLoS Pathog. 2023 Feb 17;19(2):e1011082. doi: 10.1371/journal.ppat.1011082. PMID: 36800400; PMCID: PMC9937491.

Paudel RR, Lu D, Roy Chowdhury S, Monroy EY, Wang J. Targeted Protein Degradation via Lysosomes. Biochemistry. 2023 Feb 7;62(3):564-579. doi: 10.1021/acs.biochem.2c00310. Epub 2022 Sep 21. PMID: 36130224.

Neves LL, Hair AB, Preidis GA. A systematic review of associations between gut microbiota composition and growth failure in preterm neonates. Gut Microbes. 2023 Jan-Dec;15(1):2190301. doi: 10.1080/19490976.2023.2190301. PMID: 36927287; PMCID: PMC10026866.

Martinez-Vargas M, Cebula A, Brubaker LS, Seshadri N, Lam FW, Loor M, Rosengart TK, Yee A, Rumbaut RE, Cruz MA. A novel interaction between extracellular vimentin and fibrinogen in fibrin formation. Thromb Res. 2023 Jan; 221 :97-104. doi: 10.1016/j.thromres.2022.11.028. Epub 2022 Dec 7. PMID: 36495717; PMCID: PMC9726209.

Mejia ME, Mercado-Evans V, Zulk JJ, Ottinger S, Ruiz K, Ballard MB, Britton RA, Patras KA. Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model. bioRxiv [Preprint]. 2023 Feb 9: 2023.02.09.527909. doi: 10.1101/2023.02.09.527909. PMID: 36798217; PMCID: PMC9934685.

Shen J, Wilbon AS, Zhou M, Pan Y. Mechanism of Ca<sup>2+</sup> transport by ferroportin. Elife. 2023 Jan 17; 12: e82947. doi: 10.7554/eLife.82947. PMID: 36648329; PMCID: PMC9883014.

Bijou I, Liu Y, Lu D, Chen J, Sloan S, Alinari L, Lonard DM, O'Malley BW, Wang M, Wang J. Inhibition of SRC-3 as a potential therapeutic strategy for aggressive mantle cell lymphoma. Res Sq [Preprint]. 2023 Mar 10: doi: 10.21203/ PMID: 36945511; PMCID: PMC10029087.

Joseph FM, Young NL. Histone variant-specific post-translational modifications. Semin Cell Dev Biol. 2023 Feb 15; 135: 73-84. doi: 10.1016/j.semcdb.2022.02.012. Epub 2022 Mar 9. PMID: 35277331; PMCID: PMC9458767.


2022/2023 Publications


Arielys Mendoza, Simultaneous Acquisition of Mitochondrial Calcium Retention Capacity and Swelling to Measure Permeability Transition Sensitivity. Methods Mol Biol 2022; 2497:129-140. doi: 10.1007/978-1-0716-2309-1_9

Arielys Mendoza, Keeping the beat against time: Mitochondrial fitness in the aging heart. Front Aging 2022 Jul 26;3:951417. doi: 10.3389/fragi.2022.951417

Marcus Florez, Clonal hematopoiesis: Mutation-specific adaptation to environmental change. Cell Stem Cell 2022 Jun 2;29(6):882-904. doi: 10.1016/j.stem.2022.05.006

Marcus Florez, Persistent ethnicity-associated disparity in anti-tumor effectiveness of immune checkpoint inhibitors despite equal access. Cancer Res Commun 2022:10.1158/2767-9764. CRC-21-0143. doi: 10.1158/2767-9764.CRC-21-0143

Hailey Edwards, The evolution and structure/function of bHLH-PAS transcription factor family. Biochem Soc Trans 2022 Jun 30;50(3):1227-1243. doi: 10.1042/BST20211225

Navish Bosquez Huerta, Lunatic Fringe-GFP Marks Lamina-Specific Astrocytes That Regulate Sensory Processing. J Neurosci 2022 Jan 26;42(4):567-580. doi: 10.1523/JNEUROSCI.1392-21.2021

Marlyd Mejia, Phage Resistance Accompanies Reduced Fitness of Uropathogenic Escherichia coli in the Urinary Environment. mSphere 2022 Aug 31;7(4):e0034522. doi: 10.1128/msphere.00345-22

Marlyd Mejia, Human Milk Oligosaccharides Reduce Murine Group B Streptococcus Vaginal Colonization with Minimal Impact on the Vaginal Microbiota. mSphere 2022 Feb 23;7(1):e0088521. doi: 10.1128/msphere.00885-21

Alyssa Paparella, Racial disparities in prostate cancer: A complex interplay between socioeconomic inequities and genomics. Cancer Lett 2022 Apr 10;531:71-82. doi: 10.1016/j.canlet.2022.01.028

Gary Huang, The need for unbiased genetic screens to dissect aggression in Drosophila melanogaster. Front Behav Neurosci 2022 Aug 1;16:901453. doi: 10.3389/fnbeh.2022.901453

Gabriel Escobedo, Temporal and spatially controlled APP transgene expression using Cre-dependent alleles. Dis Model Mech 2022 May 1;15(5):dmm049330. doi: 10.1242/dmm.049330

Mara Cardenas, A Costimulatory CAR Improves TCR-based Cancer Immunotherapy. Cancer Immunol Res 2022 Apr 1;10(4):512-524. doi: 10.1158/2326-6066

Sergio Aguirre, Chemotherapy Coupled to Macrophage Inhibition Induces T-cell and B-cell Infiltration and Durable Regression in Triple-Negative Breast Cancer. Cancer Res 2022 Jun 15;82(12):2281-2297. doi: 10.1158/0008-5472

Faith Joseph, Histone variant-specific post-translational modifications. Semin Cell Dev Biol 2022 Mar 9;S1084-9521(22)00051-9. doi: 10.1016/j.semcdb.2022.02.012

Andrea Ortiz, Myocardial Rev-erb-Mediated Diurnal Metabolic Rhythm and Obesity Paradox. Circulation 2022 Feb 8;145(6):448-464. doi: 10.1161/CIRCULATIONAHA.121.056076

Andrea Ortiz, Calcium/calmodulin-dependent protein kinase kinase 2 regulates hepatic fuel metabolism. Mol Metab 2022 Aug;62:101513. doi: 10.1016/j.molmet.2022.101513

Jaime Reyes, Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor. Cancer Discov 2022 Jan;12(1):220-235. doi: 10.1158/2159-8290.CD-21-0560

Jaime Reyes, Perturbed hematopoiesis in individuals with germline DNMT3A overgrowth Tatton-Brown-Rahman syndrome. Haematologica 2022 Apr 1;107(4):887-898. doi: 10.3324/haematol.2021.278990

Jaime Reyes, Constitutive loss of DNMT3A causes morbid obesity through misregulation of adipogenesis. Elife 2022 May 30;11:e72359. doi: 10.7554/eLife.72359


2020/2021 Publications


Christian Valladolid Brown, Secretion of von Willebrand Factor and Suppression of ADAMTS-13 Activity by Markedly High Concentration of Ferritin. Clin. Aopl. Thromb Hemost. 2021 PMID: 33539188

Darius Devlin, Knockout of mouse receptor accessory protein 6 leads to sperm function and morphology defects. Biol Reprod. 2020. PMID: 32101290

Jessica Felix, Ube2i deletion in adipocytes causes lipoatrophy in mice. Molecular Metabolism. 2021 PMID: 33771728

Jessica Felix, Acetyl-CoA and Metabolite Fluxes Regulate White Adipose Tissue Expansion. Trends in Endocrinology and Metabolism. 2021. PMID: 33712368

Grady Gastelum, Molecular mechanisms of pulmonary carcinogenesis by polycyclic aromatic hydrocarbons (PAHs): Implications for human lung cancer. Semin Cancer Biol. 2021 PMID: 34242741

Janet Bruno-Gaston, Prevalence of Polycystic Ovary Syndrome in Patients with McCune Albright Syndrome. 2021. PMID: 34118374

Sabrina Green, Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract. mBio 2021. PMID: 33563833

Leah Kafer, Calcium-Regulated Protein CarP Responds to Multiple Host Signals and Mediates Regulation of Pseudomonas aeruginosa Virulence by Calcium. Applied and Environmental Microbiology. 2021. PMID: 33674436

Alisha Kardian, ZFTA-RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma. Cancer Discovery. 2021. PMID: 33741710

Andrew Lopez, Dynamic Imaging of Mouse Embryos and Cardiac Development in Static Culture. Methods Mol. Biol. 2021. PMID: 32754815

Marissa Minor, Hepatitis B Virus HBx Protein Mediates the Degradation of Host Restriction Factors through the Cullin 4 DDB1 E3 Ubiquitin Ligase Complex. Cells 2020. PMID: 32235678

Oscar Murillo, Dissecting the contribution of host genetics and the microbiome in complex behaviors. Cell 2021. PMID: 33705688

Larry Scott, Jr., From Neutrophil Calcium Sensor to Myocardial Remodeling-A Double-Edged Pathway Guided by the Inflammasome. Can J. Cardiol. 2020. PMID: 32173053

Doris Taylor, Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries. ACS Infectious Disease. 2020. PMID: 32182432