2022 Student Publications

Gupta, Pawan K., JB. Allocco, JM. Fraipont, ML. McKeague, P Wang, MS. Andrade, C McIntosh, et al. "Reduced Satb1 Expression Predisposes CD4+ T Conventional Cells to Treg Suppression and Promotes Transplant Survival." PNAS, October 4, 2022 PMC9546564

Piñeros AR, Kulkarni A, Gao H, Orr KS, Glenn L, Huang F, Liu Y, Gannon M, Syed F, Wu W, Anderson CM, Evans-Molina C, McDuffie M, Nadler JL, Morris MA, Mirmira RG, Tersey SA. Proinflammatory signaling in islet β cells propagates invasion of pathogenic immune cells in autoimmune diabetes. Cell Rep. 2022 Jun 28;39(13):111011. doi: 10.1016/j.celrep.2022.111011. PMID: 35767947; PMCID: PMC9297711. 

Li Y, Girard R, Srinath A, Ciszewski C, Chen C, Lightle R, Romanos S, Moore T, Debiasse D, Antonopoulos MN, Ali H, Stadnik A, Lee JJ, Lopez-Ramirez MA, Shi C, Awad IA. Transcriptomic signatures of individual cell types in cavernous angioma. In: 18th Annual International CCM Scientific Meeting; 2022 November 17-18; Durham, NC.

Srinath A, Bindal A, Moore T, Li Y, Antonopoulos MN, DeBiasse D, Zha Y, Lightle R, Pytel P, Romanos SG, Polster SP, Girard R, Awad IA. Multiplexed Histopathological Characterization of the Cerebral Microbleed Lesional Milieu in the Aging Brain [abstract]. In: 18th Annual International CCM Scientific Meeting; 2022 November 17-18; Durham, NC.

Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Epigenetic variation impacts ancestry- associated differences in the transcriptional response to influenza infection. bioRxiv. 2022.05.10.491413; doi: https://doi.org/10.1101/2022.05.10.491413

Chen X, Pacis A, Aracena KA, Gona S, Kwan T, Groza C, Lin YL, Sindeaux R, Yotova V, Pramatarova A,Simon MM, Pastinen T, Barreiro LB, Bourque G. Transposable elements are associated with the variable response to influenza infection. bioRxiv. 2022.05.10.491101; doi: https://doi.org/10.1101/2022.05.10.491101 

Integrating genetic and oral histories of Southwest Indian populations; Arjun Biddanda, Esha Bandyopadhyay, Constanza de la Fuente Castro, David Witonsky, Nagarjuna Pasupuleti, Renée Fonseca, Suzanne Freilich, Hannah M. Moots, Jovan Stanisavic, Tabitha Willis, Anoushka Menon, Mohammed S. Mustak, Chinnappa Dilip Kodira, Anjaparavanda P. Naren, Mithun Sikdar, Niraj Rai, Maanasa Raghavan; doi: https://doi.org/10.1101/2022.07.06.498959; - in review

N. Baughan*, L. Douglas*, M. L. Giger, "Past, Present, and Future of Machine Learning and Artificial Intelligence for Breast Cancer Screening," Journal of Breast Imaging, 2022. doi:10.1093/jbi/wbac052 Invited.

H. Li, K. Robinson, L. Lan, N. Baughan, C. Chan, M. Embury, G. Whitman, R. El-Zein, I. Bedrosian, M. L. Giger, "Temporal machine learning analysis of prior mammograms for breast cancer risk prediction," Breast Cancer Research, 2022.

Chen, W.*, Brown, J. S.*, He, T., Wu, W. S., Tu, S., Weng, Z., ... & Lee, H. C. (2022). GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance. Nature Communications, 13(1):5306.

Wu, W. S.*, Brown, J. S.*, Chen, P. H., Shiue, S. C., Lee, D. E., & Lee, H. C. (2022). CLASH Analyst: A Web Server to Identify In Vivo RNA-RNA Interactions from CLASH Data. Non-coding RNA, 8(1), 6.

Milly TA, Buttner AR, Rieth N, Hutnick E, Engler ER, Campanella AR, Lella M, Bertucci MA, Tal-Gan Y. Optimizing CSP1 analogs for modulating quorum sensing in Streptococcus pneumoniae with bulky, hydrophobic nonproteogenic amino acid substitutions. RSC Chem Biol. 2022 Jan 28;3(3):301-311. doi: 10.1039/d1cb00224d. PMID: 35359494; PMCID: PMC8905529.

Simmons D, Busch SE, Titley H, Grasselli G, Shih J, Du X, Wei C, Gomez CM, Piochon C, Hansel C. (2022) Sensory over-responsivity and aberrant plasticity in cerebellar cortex in a mouse model of syndromic autism. Biological Psychiatry: Global Open Science, 2(4): 450-459. https://doi.org/10.1016/j.bpsgos.2021.09.004

Medalla M., Chang W, Ibanez, S, Guillamon-Vivancos T, Nittman M, Kapitokonova A, Busch SE, Rosene D, Moore TL, Luebke JI. (2022) Layer-specific pyramidal neuron properties underlie diverse anterior cingulate cortical motor and limbic networks. Cerebral Cortex, 32(10): 2170-2196. https://doi.org/10.1093/cercor/bhab347

Carlson MO, Rice DP, Berg JJ, and Steinruecken M. (2022). Polygenic score accuracy in ancient samples: Quantifying the effects of allelic turnover. PLOS Genetics. 18(5):e1010170.

Ahmed, S., Chowdhury, M. A. H., Kader, S. B., Shahriar, M. H., Begum, B. A., Eunus, M., ... & Yunus, M. (2022). Personal exposure to household air pollution and lung function in rural Bangladesh: A population-based cross-sectional study. International Journal of Environmental Health Research, 1-13.

Raqib, R., Akhtar, E., Sultana, T., Ahmed, S., Chowdhury, M. A. H., Shahriar, M. H., ... & Yunus, M. (2022). Association of household air pollution with cellular and humoral immune responses among women in rural Bangladesh. Environmental Pollution, 299, 118892. 

Kamenar, K., Hossen, S., Gupte, A. N., Siddharthan, T., Pollard, S., Chowdhury, M., ... & Checkley, W. (2022). Previous tuberculosis disease as a risk factor for chronic obstructive pulmonary disease: a cross-sectional analysis of multicountry, population-based studies. Thorax, 77(11), 1088-1097.

The Journal of Immunology, 207(5), 1265-1274. Canaria, D. A., Clare, M. G., Yan, B., Campbell, C. B., Ismaio, Z. A., Anderson, N. L., ... & Olson, M. R. (2022). IL-1β promotes IL-9-producing Th cell differentiation in IL-2-limiting conditions through the inhibition of BCL6. Frontiers in Immunology, 6692.

Dehua Bi, Meizi Liu, Rachael Liu, Jianchang Lin. (2022) "BEATS: Bayesian Hybrid Design with Flexible Sample Size Adaptation for Time-To-Event Endpoints". Submitted to Stats.Med.

Xiaolei Lin, Jiaying Lyu, Shijie Yuan, Dehua Bi, Sue-Jane Wang, and Yuan Ji. (2022) "Bayesian Sample Size Planning Tool for Phase I Dose- Finding Trials." JCO Precision Oncology, 2022, 6: e2200046.

Je Yeong Sone, Nicholas Hobson, Abhinav Srinath, Sharbel G Romanos, Ying Li, Juli ́an Carrion Penagos, Abdallah Shkoukani, Agnieszka Stadnik, Kristina Piedad, Rhonda Lightle, Thomas Moore, Dorothy DeBiasse, Dehua Bi, Robert Shenkar, Timothy Carroll, Yuan Ji, Romuald Girard, and Issam A Awad. (2022) "Perfusion and permeability MRI predicts future cavernous angioma hemorrhage and growth." Journal of Magnetic Resonance Imaging 55 (5), 1440-1449

Sharbel G Romanos, Abhinav Srinath, Ying Li, Bingqing Xie, Chang Chen, Yan Li, Thomas Moore, Dehua Bi, Je Yeong Sone, Rhonda Lightle, Nick Hobson, Dongdong Zhang, Janne Koskim ̈aki, Le Shen, Sara McCurdy, Catherine Chinhchu Lai, Agnieszka Stadnik, Kristina Piedad, Juli ́an Carrion-Penagos, Abdallah Shkoukani, Daniel Snellings, Robert Shenkar, Dinanath Sulakhe, Yuan Ji, Miguel A Lopez-Ramirez, Mark L Kahn, Douglas A Marchuk, Mark H Ginsberg, Romuald Girard, and Issam A Awad. (2022)

Zorova LD, Demchenko EA, Korshunova GA, Tashlitsky VN, Zorov SD, Andrianova NV, Popkov VA, Babenko VA, Pevzner IB, Silachev DN, Plotnikov EY, Zorov DB. Is the Mitochondrial Membrane Potential (∆Ψ) Correctly Assessed? Intracellular and Intramitochondrial Modifications of the ∆Ψ Probe, Rhodamine 123. Int J Mol Sci. 2022 Jan 1;23(1):482. doi: 10.3390/ijms23010482. PMID: 35008907; PMCID: PMC8745654.

Popkov VA, Zharikova AA, Demchenko EA, Andrianova NV, Zorov DB, Plotnikov EY. Gut Microbiota as a Source of Uremic Toxins. Int J Mol Sci. 2022 Jan 1;23(1):483. doi: 10.3390/ijms23010483. PMID: 35008909; PMCID: PMC8745165.

Baughan N*, Douglas L*, Giger ML. (2022). Past, present, and future of machine learning and artificial intelligence for breast cancer screening. Journal of Breast Imaging 4(5): 451-459.

Michael K. Yu*, Emily C. Fogarty*, A. Murat Eren. "The genetic and ecological landscape of plasmids in the human gut." 2022. Nature Microbiology.

Florian Trigodet, Karen Lolans, Emily C. Fogarty, Alon Shaiber, Hilary G. Morrison, Luis Barreiro, Bana Jabri, A. Murat Eren. "High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes". 2022. Molecular Ecology Resources.

Kaiser C, Bradu A, Gamble N, Caldwell JA, Koh AS. AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression. Immunol Rev. 2022 Jan;305(1):59-76. doi: 10.1111/imr.13026. Epub 2021 Sep 20. PMID: 34545959; PMCID: PMC9250823.

Wei, J.†, Yu, X. †, Yang, L. †, Liu, X. †, Gao, B., et al. (2022). FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development. Science, 376(6596): 968-973. doi: 10.1126/science.abe9582. 

Pal, P., Millner, A., Semina, S.E., Huggins, R.J., et al. Endocrine therapy-resistant breast cancer cells are more sensitive to ceramide kinase inhibition and elevated ceramide levels than therapy-sensitive breast cancer cells. Cancers (2022).

Semina, S.E., Pal, P., Kansara, N.S., Huggins, R.J., et al. Selective pressure of endocrine therapy activates the integrated stress response through NFκB signaling in a subpopulation of ER positive breast cancer cells. Breast Cancer Research (2022).

Kim, Hyunkyung, Kenneth Westerman, Kirk Smith, Joshua Chiou, Joanne Cole, Tim Majarian, Marcin von Grotthuss, Josep Mercader, Soo Heon Kwak, Jaegil Kim, Jose Florez, Kyle Gaulton, Alisa Manning, and Miriam Udler, "High-throughput Genetic Clustering of Type 2 Diabetes Loci Reveals Heterogeneous Mechanistic Pathways of Metabolic Disease," Diabetologia, 2022.

Felix Vaura, Hyunkyung Kim, Miriam Udler, Veikko Salomaa, Leo Lahti, and Teemu Niiranen, "Multi-Trait Genetic Analysis Reveals Clinically Interpretable Hypertension Subtypes," Circulation: Genomic and Precision Medicine, 2022.

Adé K, Saenz Coronilla J, Obino D, Weinberger T, Kaiser C, Mella S, Chen C, Katsimpardi L, Werts C, Li H et al. (2022) Inflammation drives age-induced loss of tissue resident macrophages. BioRxiv preprint, 10.1101/2022.10.02.510513.

Kramer, C., et al. (2022). Dynamic task-belief is an integral part of decision-making. PMCID: PMC9357195

Kroll K., French A. R., Sosnick T. R., Rock R. S (2022). LILAC: Enhanced actin imaging with an optogenetic Lifeact. bioRxiv. https://doi.org/10.1101/2022.04.07.487416

Kiefl E., Esen O. C., Miller S. E., Kroll K.L., Willis A. D., Rappé M. S., Pan T., ErenA. M (2022). Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. bioRxiv. https://doi.org/10.1101/2022.03.02.482602

MacDonald, M.E., Weathered, R.K., Stewart, E.C., Magold, A.I., Mukherjee, A., Gurbuxani, S., Smith, H., et al. (2022). Lymphatic coagulation and neutrophil extracellular traps in lung-draining lymph nodes of COVID-19 decedents. Blood Advances, 6(24) 6249-6262. PMCID: PMC9394105

Matthews JM, Schuster B, Kashaf SS, Liu P, Ben-Yishay R, Ishay-Ronen D, Izumchenko E, Shen L, Weber CR, Bielski M, Kupfer SS, Bilgic M, Rzhetsky A, Tay S. OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics. PLoS Comput Biol. 2022 Nov 9;18(11):e1010584. doi: 10.1371/journal.pcbi.1010584. PMID: 36350878; PMCID: PMC9645660.

Muhtaseb AW, Duan J. Modeling common and rare genetic risk factors of neuropsychiatric disorders in human induced pluripotent stem cells. Schizophr Res. 2022 Apr 19:S0920-9964(22)00156-6. doi: 10.1016/j.schres.2022.04.003. Epub ahead of print. PMID: 35459617; PMCID: PMC9735430.

Plessier F, Schmutz S, Novault S, Marlow H. Single-Cell Transcriptomic Analysis in the Regenerating Cnidarian Nematostella vectensis. Methods Mol Biol. 2022;2450:565-581. doi: 10.1007/978-1-0716-2172-1_30. PMID: 35359329; PMCID: PMC9761532.

Downey J, Randolph HE, Pernet E, Tran KA, Khader SA, King IL, Barreiro LB, Divangahi M. Mitochondrial cyclophilin D regulates disease tolerance by licensing NK cell development and IL-22 production during influenza virus infection. Cell Reports. 2022, 39:110974. doi: 10.1016/j.celrep.2022.110974. PMID: 35732121.

Labrosse R, Boufaied I, Bourdin B, Gona S, Randolph HE, Logan BR, Bourbonnais S, Berthe C, et al. Aberrant T cell activation and exhaustion in SCID survivors with poor T- cell reconstitution post-transplant. Journal of Allergy and Clinical Immunology. 2022, S0091-6749(22)01057-0. doi: doi: 10.1016/j.jaci.2022.08.004. PMID: 35987350.

Melcher L, Rennert E, Ross J, Rust M, Robertson-Anderson R, Das M. Sustained order-disorder transitions in a model colloidal system driven by rhythmic crosslinking. Soft Matter. 2022 Apr 13;18(15):2920-2927. doi: 10.1039/d1sm01583d. PMID: 35343534.

Shastry V, Bell KL, Buerkle CA, Fordyce JA, Forister ML, Gompert Z, Lebeis SL, Lucas LK, Marion ZH, Nice CC. A continental-scale survey of Wolbachia infections in blue butterflies reveals evidence of interspecific transfer and invasion dynamics. G3 (Bethesda). 2022 Sep 30;12(10):jkac213. doi: 10.1093/g3journal/jkac213. PMID: 35976120; PMCID: PMC9526071.

Hagan MJ, Shenkar R, Srinath A, Romanos SG, Stadnik A, Kahn ML, Marchuk DA, Girard R, Awad IA. Rapamycin in Cerebral Cavernous Malformations: What Doses to Test in Mice and Humans. ACS Pharmacol Transl Sci. 2022 Apr 25;5(5):266-277. doi: 10.1021/acsptsci.2c00006. PMID: 35592432; PMCID: PMC9112291.

Steiner, M.C. and Novembre, J. “Population genetics models for the spatial spread of adaptive alleles: a review in light of the COVID-19 pandemic. PLoS Genetics, 18(9): e1010391. (2022). PMCID: PMC9498967

M.E. MacDonald, R.K. Weathered, E.C. Stewart, et. al. Lymphatic coagulation and neutrophil extracellular traps in lung-draining lymph nodes of COVID-19 decedents. Blood Advances. (2022).

Ben-Oren, Y., Strassberg, S. S., Hovers, E., Kolodny, O., & Creanza, N. (2022). Modeling effects of inter-group contact on links between population size and cultural complexity. bioRxiv. In press.

Swank S, Elazegui E, Janidlo S, Sanger TJ, Bell MA, Stuart YE. (2022). Attempting genetic inference from directional asymmetry during convergent hindlimb reduction in squamates. Ecol Evol. 12(7):e9088. doi: 10.1002/ece3.9088. PMID: 35845359; PMCID: PMC9280442.

Arvanitis M, Tayeb K, Strober BJ, Battle A. Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity. Am J Hum Genet. 2022 Feb 3;109(2):223-239. doi: 10.1016/j.ajhg.2022.01.002. Epub 2022 Jan 31. PMID: 35085493; PMCID: PMC8874223.

Billault-Chaumartin I, Michon L, Anderson CA, Yde SE, Suarez C, Iwaszkiewicz J, Zoete V, Kovar DR, Martin SG. Actin assembly requirements of the formin Fus1 to build the fusion focus. J Cell Sci. 2022 Jul 1;135(13):jcs260289. doi: 10.1242/jcs.260289. Epub 2022 Jul 8. PMID: 35673994; PMCID: PMC9377709.