2021 Student Publications


Adegunsoye A, Morisset J, Newton CA, Oldham JM, Vittinghoff E, Linderholm AL, Strek ME, Noth I, Garcia CK, Wolters PJ, Ley B. (2021). Leukocyte telomere length and mycophenolate therapy in chronic hypersensitivity pneumonitis. Eur Respir J 57 (3):2002872. PMID: 33122338 PMCID: PMC8104021.


Ning K, Song E, Sendayen B, Prosseda P, Chang K, Ghaffarieh A, Alvarado JA, Wang B, Berbari N, Hu Y, and Sun Y. (2021). Defective INPP5E distribution In NPHP1-related Senior-Løken Syndrome. Molecular Genetics & Genomic Medicine 1: e1566. PMID: 33306870.


Alvarado W, Perez-Lemus GR, Menéndez CA, Byléhn F, de Pablo JJ. (2021). Molecular characterization of COVID-19 therapeutics: Luteolin as an allosteric modulator of the spike protein of SARS-CoV-2. Molecular Systems Design & Engineering. DOI:10.1039/D1ME00119A.

Alvarado W, Moller J, Ferguson AL, de Pablo JJ. (2021). Tetranucleosome Interactions Drive Chromatin Folding. ACS Central Science. DOI:10.1021/acscentsci.1c00085.

Byléhn F, Menéndez CA, Perez-Lemus GR, Alvarado W, de Pablo JJ. (2021). Modeling the binding mechanism of remdesivir, favilavir, and ribavirin to SARS-CoV-2 RNA-dependent RNA polymerase. ACS Central Science. https://doi.org/10.1021/acscentsci.0c01242. 


Groza C, Chen X, Pacis A, Simon MM, Pramatarova A, Aracena KA, Pastinen T, Barreiro LB, Bourque G. Genome graphs detect human polymorphisms in active epigenomic state during influenza infection. bioRxiv. 2021.09.29.462206; doi: https://doi.org/10.1101/2021.09.29.462206 


McArdel, S. L., [...], Bayhi, N., et al. Anti-tumor effects of RTX-240: an engineered red blood cell expressing 4-1BBL and IL-15. Cancer Immunol Immunother 70, 2701-2719 (2021). PMC8360899 

 Zhang, X., [...], Bayhi, N., et al. Engineered red blood cells as an off-the-shelf allogeneic anti-tumor therapeutic. Nat Commun 12, 2637 (2021). DOI: 10.1038/s41467-021-22898-3. PMC8113241


Sone JY, Li Y, Hobson N, Romanos SG, Srinath A, Lyne SB, Shkoukani A, Carrión-Penagos J, Stadnik A, Piedad K, Lightle R, Moore T, Li Y, Bi D, Shenkar R, Carroll T, Ji Y, Girard R, Awad IA. (2021). Perfusion and permeability as diagnostic biomarkers of cavernous angioma with symptomatic hemorrhage[J]. Journal of Cerebral Blood Flow & Metabolism 41(11):2944-2956. DOI: 10.1177/0271678X211020587.

Bi D, Sengupta S, Zhou T, Ji Y. (2021). Mutstats: An Ultra-fast Computational Method to Determine Clonal Status of Somatic Mutations, Journal Data Science Volume 19, Issue 3 465–484. DOI 10.6339/21-JDS1016.


Blanc, J., Kremling, K. A., Buckler, E., and Josephs, E. B. (2021). Local adaptation contributes to gene expression divergence in maize. G3, 11(2):jkab004 PMID: 33604670 


Calderazzo S, Busch SE, Moore TL, Rosene DL, Medalla M. (2021) Distinct distribution of medial temporal and premotor inputs and outputs in the primate anterior cingulate cortex. Journal of Comparative Neurology, 529: 885-904. https://doi.org/10.1002/cne.24986 


Milly TA, Engler ER, Chichura KS, Buttner AR, Koirala B, Tal-Gan Y, Bertucci MA. Harnessing Multiple, Nonproteogenic Substitutions to Optimize CSP:ComD Hydrophobic Interactions in Group 1 Streptococcus pneumoniae. Chembiochem. 2021 Jun 2;22(11):1940-1947. doi: 10.1002/cbic.202000876. Epub 2021 Apr 7. PMID: 33644965.


Calzada Preston, C. E., Pruett-Jones, S., & Eberhard, J. R. (2021). Monk Parakeets as a Globally Naturalized Species. Naturalized Parrots of the World: Distribution, Ecology, and Impacts of the World's Most Colorful Colonizers, 173-192.

Calzada Preston, C. E., & Pruett-Jones, S. (2021). The number and distribution of introduced and naturalized parrots. Diversity, 13(9), 412.


Canaria, D. A., Yan, B., Clare, M. G., Zhang, Z., Taylor, G. A., Boone, D. L., ... & Olson, M.R. (2021). STAT5 Represses a STAT3-independent Th17-like program during Th9 cell differentiation. The Journal of Immunology, 207(5), 1265-1274. 


Stajich JE, Vu AL, Judelson HS, Vogel GM, Gore MA, Carlson MO, Devitt N, Jacobi J, Mudge J, Lamour KH, Smart CD. (2021). High quality reference genome sequence for the oomycete vegetable pathogen Phytophthora capsici strain LT1534. Microbiology Resource Announcements. 10(21):e00295-21. 

Carlson MO, Montilla-Bascon G, Hoekenga OA, Tinker NA, Poland J, Baseggio M, Sorrells ME, Jannink JL, Gore MA and Yeats TH. (2019). Multivariate genome-wide association analyses reveal the genetic basis of seed fatty acid composition in oat (Avena sativa l.). G3: Genes, Genomes,Genetics. 9(9):2963-2975.


Arias-Cavieres, A; Fonteh, A; Castro-Rivera CI; Garcia, AJ III. (2021). Intermittent Hypoxia causes targeted disruption to NMDA receptor dependent synaptic plasticity in area CA1 of the hippocampus. Exp Neurol., 344, 113808. PMID: 34256046 


Céspedes-Arias, L. N., Cuervo, A. M., Bonaccorso, E., Castro-Farias, M., Mendoza-Santacruz, A., Pérez-Emán, J. L., ... & Cadena, C. D. (2021). Extensive hybridization between two Andean warbler species with shallow divergence in mtDNA. The Auk, 138(1), ukaa065.

Fialko, Kristina, Jarome R. Ali, Laura Cespedes Arias, Jacob Drucker, Klara K. Norden, Trevor Price, Rosalyn Price-Waldman, and Stephen Pruett-Jones. "The Sensory Ecology of Birds." (2021).

Arias, Laura N. Céspedes. "Digest: Selection for staggered pollen release as a driver of heteranthery." (2021): 2944-2945


Greig, J. A., Jennis, M., Dandekar, A., Chorazeczewski, J. K., Smith, M. K., Ashley, S. N., ... & Wilson, J. M. (2021). Muscle-directed AAV gene therapy rescues the maple syrup urine disease phenotype in a mouse model. Molecular Genetics and Metabolism, 134(1-2), 139-146. PMID: 34454844


Shahriar, M. H., Chowdhury, M. A. H., Ahmed, S., Eunus, M., Kader, S. B., Begum, B. A., ... & Yunus, M. (2021). Exposure to household air pollutants and endothelial dysfunction in rural Bangladesh: a cross-sectional study. Environmental Epidemiology, 5(2) 

Ahmed, S., Ibrahimou, B., Kader, S. B., Chowdhury, M. A. H., Ahsan, H., & Yunus, M. (2021). Household biomass fuel use is associated with chronic childhood malnutrition: Result from a nationwide cross‐sectional survey in Bangladesh. Indoor air, 31(6), 2167-2175.


Canaria, D. A., Yan, B., Clare, M. G., Zhang, Z., Taylor, G. A., Boone, D. L., ... & Olson, M. R. (2021). STAT5 Represses a STAT3-independent Th17-like program during Th9 cell differentiation. 


Dehua Bi, Subhajit Sengupta, Tianjian Zhou, and Yuan Ji. (2021) "Mutstats: An Ultra-fast Computational Method to Determine Clonal Status of Somatic Mutations." Journal of Data Science 19, no.3 (2021)

Je Yeong Sone, Yan Li, Nicholas Hobson, Sharbel G Romanos, Abhinav Srinath, Se ́an B Lyne, Abdallah Shkoukani, Juli ́an Carrion Penagos, Agnieszka Stadnik, Kristina Piedad, Rhonda Lightle, Thomas Moore, Ying Li, Dehua Bi, Robert Shenkar, Timothy Carroll, Yuan Ji, Romuald Girard, and Issam A Awad. (2021) "Perfusion and permeability as diagnostic biomarkers of cavernous angioma with symptomatic hemorrhage." Journal of Cerebral Blood Flow & Metabolism. 2021, 41(11): 2944-2956. 


Joslin, A.C., Sobreira, D.R., Hansen, G.T., Sakabe, N., Aneas, I., Montefiori, L.E., Farris, K.M., Qiao, M., Lehman, D., Ober, C., N obrega, M.A. A functional genomics pipeline identifies pleiotropy and cross-tissue effects within obesity-associated GWAS loci. Nature Communications 12, 5253 (2021).

Sobreira, D.R., Joslin, A.C., Zhang, Q., Williamson, I., Hansen, G.T., Farris, K.M., Sakabe, N.J., Bozek, G., Jensen-Cody, S.O., Flippo, K.H., Ober, C., Bickmore, W.A., Potthoff, M., Chen, M., Aneas, I., Nobrega, M.A. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5. Science (2021).


Elizabeth Landis, Emily C Fogarty, John Edwards, Otilia Popa, A. Murat Eren, and Benjamin Wolfe. "Microbial diversity and interaction specificity in kombucha tea fermentations" 2021. MSystems.

A. Murat Eren, Evan Kief, Alon Shaiber, Iva Veseli, Samuel E. Miller, Matthew S. Schechter, Isaac Fink, Jessica N. Pan, Mahmoud Yousef, Emily C. Fogarty, et al. "Community-led, integrated, reproducible multi-omics with anvi'o". (2021). Nature Microbiology.


Ghulam-Jelani Z, Barrios-Martinez J, Eguiluz-Melendez A, Gomez R, Anania Y, Yeh FC. (2021). Redundancy Circuits of the Commissural Pathways in Human and Rhesus Macaque Brains. Human Brain Mapping. doi: https://doi.org/10.1002/hbm.25363


Kaiser C*, Bradu A*, Gamble N*, Caldwell J.A, Koh A.S. (2021) AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression. Immunological Reviews, 10.1111/imr.13026 (PMCID: PMC9250823).


Wildenberg, G. A., Rosen, M. R., Lundell, J., Paukner, D., Freedman, D. J., & Kasthuri, N. (2021). Primate neuronal connections are sparse in cortex as compared to mouse. Cell Reports, 36(11), 109709. PMID: 34525373


Logan, C.N., Roja, G., Wilkinson, C.S., Polo Escorcia, A.K., Reichel, C.M., Peris, J., Knackstedt, L.A. (2021). Systemic oxytocin increases glutamate efflux in the nucleus accumbens core of cocaine-experienced male and female rats but only increases dopamine efflux in males. Behav Brain Res. 24;417:113590. doi: 10.1016/j.bbr.2021.113590. Epub ahead of print. PMID: 34551348.


Surette, F.A., Guthmiller, J.J., Li, L., Sturtz, A.J., Vijay, R., Pope, R.L., et al. (2021). Extrafollicular CD4 T cell-derived IL-10 functions rapidly and transiently to support anti-Plasmodium humoral immunity. PLOS Pathogens 17(2): e1009288.

Vijay, R., Jenna, J., Guthmiller, A.J., Sequoia, C., Johnson, J.T., Lei L., Lan, L.Y-L., Pope, R.L., Yani, C., Rogers, K.J., Dutta, N., Toombs, J.E., Wilson, M.E., Wilson, P.C., Maury, W., Brekken. R.A., Butler, N.S. (2021). Hemolysis-associated phosphatidylserine exposure promotes polyclonal plasmablast differentiation. J Exp Med; 218 (6): e20202359.


Ciebiera, M., Esfandyari, S., Siblini, H., Prince, L., Elkafas, H., Wojtyła, C., Al-Hendy, A., Ali, M. (2021). Nutrition in Gynecological Diseases: Current Perspectives. Nutrients, 13(4):1178. doi: 10.3390/nu13041178. PMID: 33918317; PMCID: PMC8065992.


Lai, B., Qian, S., Zhang, H., Zhang, S., Kozlova, A., Duan, J., He, X., Xu, J. (2021). Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning, bioRxiv 2021.02.02.429064


Yates, J.A., Valtueña A.A., Vågene, Å.J., Cribdon, B., Velsko, I.M., Borry, M., Bravo-Lopez, M.J., Fernandez-Guerra, A., Green, E.J., Ramachandran, S.L., Heintzman, P.D., Spyrou, M.A., Hübner, A., Gancz, A.S., Hider, J., Allshouse, A.F., Zaro, V., Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data, 8(1):31. doi: 10.1038/s41597-021- 00816-y. PMID: 33500403; PMCID: PMC7838265.


Randolph HE, Fiege JK, Thielen BK, Mickelson CK, Shiratori M, Barroso-Batista J, Langlois RA, Barreiro LB. Genetic ancestry effects on the response to viral infection are pervasive but cell type-specific. Science. 2021, 374:1127-1133. doi: 10.1126/science.abg0928. PMID: 34822289.


Bashirzadeh, Y., Redford, S.A., Lorpaiboon, C., Groaz, A., Litschel, T., Schwille, P., Hocky, G.M., Dinner, A.R., and Liu, A.P. (2021). "Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture." Communications Biology.

Scheff, D.R., Redford, S.A., Lorpaiboon, C., Majumdar, S., Dinner, A.R., Gardel, M.L. (2021). "Actin filament alignment causes mechanical hysteresis in cross-linked networks." Soft Matter.

Jonathan, C., Han, M., Zhang, R., Redford, S.A., Lemma, L.M., Morgan, L., Ruijgrok, P.V. et al. (2021). "Machine learning active-nematic hydrodynamics." PNAS (usa).

Zhang, R., Redford, S.A., Ruijgrok, P.V., Kumar, N., Mozaffari, A., Zemsky, S., Dinner, A.R., et al. (2021). "Spatiotemporal control of liquid crystal structure and dynamics through activity patterning." Nature Materials 20, no. 6: 875-882.


Wildenberg, G. A., Rosen, M.C., R., Lundell, J., Paukner, D., Freedman, D. J., & Kasthuri, N. (2021). Primate neuronal connections are sparse in cortex as compared to mouse. Cell Reports, 36(11), 109709.


Borowska, M. T., Drees, C., Yarawsky, A. E., Viswanathan, M., Ryan, S.M., Bunker, J.J., Herr, A. B., Bendelac, A., Adams, E. J. (2021). The Molecular Characterization of Antibody Binding to a Superantigen-like Protein from a Commensal Microbe. PNAS.


Shah, A., Mittleman, B.E., Gilad, Y. et al. (2021). Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol 22, 291. https://doi.org/10.1186/s13059-021-02502-z


Alzate-Correa, D., Liu, J.M., Jones, M., Silva, T.M., Alves, M.J., Burke, E., Zuñiga, J., Kaya, B., Zaza, G., Aslan, M.T., Blackburn, J., Shimada, M.Y., Fernandes-Junior, S.A., Baer, L.A., Stanford, K.I., Kempton, A., Smith, S., Szujewski, C.C., Silbaugh, A., et al. (2021). Neonatal apneic phenotype in a murine congenital central hypoventilation syndrome model is induced through non-cell autonomous developmental mechanisms. Brain Pathol (1):84-102. PMID: 32654284 Silbaugh, A., Vallin, J., Pelaez, F., Kim, M., Shao, Q., Lee, H., Bischof, J.C., Azarin, S.M. (2021). Enhancing electroporation-induced liposomal drug release in suspension and solid phases. Journal of Controlled Release (under review)


Simonett, S.P., Shin, S., Bacher, R., Herring, J.A., Smith, L.A., Dong, C., Rabaglia, M.E., Stapleton, D.S., Schueler, K.L., Choi, J., Bernstein, M.N., et al. (2021). "Identification of direct transcriptional targets of Nfatc2 that promote -cell proliferation". The Journal of Clinical Investigation.


MacDonald, M.E., Weathered, R.K., Stewart, E.C., et. al. (2021). Lymphatic coagulation and neutrophil extracellular traps in lung draining lymph nodes of COVID-19 decedents.


Khuu, M.A., Nallamothu, T., Castro-Rivera, C., Arias-Cavieres, A., Szujewski, C.C., Garcia, A.J. (2021). Stage-dependent effects of intermittent hypoxia influence the outcome of hippocampal adult neurogenesis. Scientific Reports.


Molina, Y., San Miguel, L.G., Tamayo, L.I., Pichardo, C.M., Torres, P., et al. (2021). Comparing different interventions' effects on Latinas' screening mammography and participant-driven information diffusion. In Press. Health Education & Behavior. (PMID: 34041942)


Eren, A.M., Kiefl, E., Shaiber, A., Veseli, I., et al. (2021). Community-led, integrated, reproducible multi-omics with anvi'o. Nat Microbiol 6, 3-6. https://doi.org/10.1038/s41564-020-00834-3


Voisine, J., Abadie, V. (2021). Interplay Between Gluten, HLA, Innate and Adaptive Immunity Orchestrates the Development of Coeliac Disease. Front Immunol, 12, 674313. PMCID: PMC8206552. https://doi.org/10.3389/fimmu.2021.674313

Im, N.G., Guillaumet-Adkins, A., Wal, M., Rogers, A.J., Voisine, J., et al. (2021). Regulatory programs of B-cell activation and germinal center reaction allow for B- ALL escape from CD19 CAR T-cell therapy. Cancer Immunology Research.


Klawon, D.E.J., Gilmore, D.C., Leonard, J.D., Miller, C.H., Walker, M.T., et al. (2021). Altered selection on a single self-ligand promotes susceptibility to organ-specific T cell infiltration. J Exp Med. 218(6):e20200701. doi: 10.1084/jem.20200701. PMID: 33914024; PMCID: PMC8091134.

Chao, J.L., Korzinkin, M., Zhavoronkov, A., Ozerov, I.V., Walker, M.T., Higgins, K., et al. (2021). Effector T cell responses unleashed by regulatory T cell ablation exacerbate oral squamous cell carcinoma. Cell Rep Med. 2(9):100399. doi: 10.1016/j.xcrm.2021.100399. PMID: 34622236; PMCID: PMC8484691.


Yesilkanal, A. E., Yang, D., Valdespino, A., Tiwari, P., Sabino, A. U., Nguyen, L. C., Rosner, M. R., et al. (2021). Limited inhibition of multiple nodes in a driver network blocks metastasis. Elife, 10, e59696.

Nguyen, L. C., Yang, D., Nicolaescu, V., Best, T., Chen, S., Friesen, J. B., Rosner, M. R., et al. (2021). Cannabidiol inhibits SARS-CoV-2 replication and promotes the host innate immune response. BioRxiv.


Yde SE, Kadzik RS, Kovar DR. Stir it up: The role of actin in mitochondrial mixing during mitosis. Dev Cell. 2021 Apr 19;56(8):1080-1082. doi: 10.1016/j.devcel.2021.03.028. PMID: 33878298.


Kerr, W.T., Zhang, X., Hill, C.E., Janio, E.A., Chau, A.M., Braesch, C.T., Le, J.M., et al. (2021). "Epilepsy, dissociative seizures, and mixed: Associations with time to video- EEG." Seizure 86: 116-122. PMCID: PMC7979505

Kerr, W.T., Zhang, X., Hill, C.E., Janio, E.A., Chau, A.M., Braesch, C.T., Le, J.M., et al. (2021). "Factors associated with delay to video-EEG in dissociative seizures." Seizure 86: 155-160. PMCID: PMC8006748

Kerr, Wesley T., Xingruo Zhang, Emily A. Janio, Amir H. Karimi, Corinne H. Allas, Ishita Dubey, Siddhika S. Sreenivasan et al. (2021). "Reliability of additional reported seizure manifestations to identify dissociative seizures." Epilepsy & Behavior 115: 107696. PMCID: PMC7882023


Zhou, Y., Bastian, I.N., Long, M.D., Dow, M., Li, W., Liu, T., Ngu, R.K., Antonucci, L., Huang, J.Y., et al. (2021). Activation of NF-κB and p300/CBP potentiates cancer chemoimmunotherapy through induction of MHC-I antigen presentation. Proceedings of the National Academy of Sciences, 118 (8) e2025840118; DOI: 10.1073/pnas.2025840118


McCarthy, G.M., Blasio, A., Donovan, O.G., Schaller, L.B., Zsengeller, Z.K., Subramanian, B., Ziolkowski, L., et al. (2021). Recessive, gain-of-function toxicity in an APOL1 BAC transgenic mouse model mirrors human APOL1 kidney disease. Dis Model Mech. 14(8):dmm048952. doi: 10.1242/dmm.048952. Epub 2021 Aug 5. PMID: 34350953; PMCID: PMC8353097.

Springer, M.Z., Poole, L.P., Drake, L.E., Ziolkowski, L., et al. (2021). BNIP3-dependent mitophagy promotes cytosolic localization of LC3B and metabolic homeostasis in the liver. Autophagy. 1-17. doi: 10.1080/15548627.2021.1877469. Epub ahead of print. PMID: 33459136.

Berardi, D., Bock-Hughes, A., Drake, L., Ziolkowski, L., et al. (2021). BNIP3 attenuates hepatocellular carcinoma by promoting lipid droplet turnover at the lysosome. [https://doi.org/10.21203/rs.3.rs-947988/v1]

Poole, L.P., Ziolkowski, L., Bock-Hughes, A., Berardi, D.E., et al. (2021). ULK1 Promotes Mitophagy via Phosphorylation and Stabilization of BNIP3. Research Square [https://doi.org/10.21203/rs.3.rs-551227/v1]


Homa, K.E., Zsolnay, V., Anderson, C.A., O'Connell, M.E., Neidt, E.M., Voth, G.A., Bidone, T.C., Kovar, D.R. (2021). Formin Cdc12's Specific Actin Assembly Properties are Tailored for Cytokinesis in Fission Yeast, Biophys. J. 120, 2984-2997. DOI: 10.1016/j.bpj.2021.06.023 PMCID: 34214524