2023 Student Publications

Kordon SP, Dutka P, Adamska JM, Bandekar SJ, Leon K, Erramilli SK, Adams B, Li J, Kossiakoff AA, Araç D. Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder. Nat Commun. 2023 Feb 6;14(1):635. doi: 10.1038/s41467-023-36312-7. PMID: 36746957; PMCID: PMC9902482.

Ahmad-Gawel M. Digest: Complex dynamics of speciation and implications for macroevolutionary models. Evolution. 2023 Jun 29;77(7):1732-1733. doi: 10.1093/evolut/qpad088. PMID: 37195719. 

Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biol Evol. 2023 May 12;15(5):evad081. doi: 10.1093/gbe/evad081. Epub ahead of print. PMID: 37170918; PMCID: PMC10210621.

Binder AK, Peecher DL, Qvigstad AJ, Gutierrez SD, Magaña J, Banks DB, Korach KS. Differential Strain-dependent Ovarian and Metabolic Responses in a Mouse Model of PCOS. Endocrinology. 2023 Feb 11;164(4):bqad024. doi: 10.1210/endocr/bqad024. PMID: 36718579; PMCID: PMC10208753.
 

Li H, Robinson K, Lan L, Baughan N, Chan CW, Embury M, Whitman GJ, El-Zein R, Bedrosian I, Giger ML. Temporal Machine Learning Analysis of Prior Mammograms for Breast Cancer Risk Prediction. Cancers (Basel). 2023 Apr 4;15(7):2141. doi: 10.3390/cancers15072141. PMID: 37046802; PMCID: PMC10093086.

Rubien-Thomas E, Berrian N, M Rapuano K, J Skalaban L, Cervera A, Nardos B, Cohen AO, Lowrey A, M Daumeyer N, Watts R, Camp NP, Hughes BL, Eberhardt JL, Taylor-Thompson KA, Fair DA, Richeson JA, Casey BJ. Uncertain threat is associated with greater impulsive actions and neural dissimilarity to Black versus White faces. Cogn Affect Behav Neurosci. 2023 Feb 2. doi: 10.3758/s13415-022-01056-2. Epub ahead of print. PMID: 36732466.
McIntosh, C. M., Allocco, J., Wang, P., McKeague, M., Wang, Y., Cassano, A., Xie, S., Cartin, R. M., Chen, L., Sattar, H., Yin, D., Zhang, Z., Chong, A., Alegre, M. L. (2023). Heterogeneity in allospecific T cell function in transplant tolerant hosts determines susceptibility to rejection following infection. Manuscript submitted for publication.

Della Libera K, Strandburg-Peshkin A, Griffith SC, Leu ST. Fission-fusion dynamics in sheep: the influence of resource distribution and temporal activity patterns. R Soc Open Sci. 2023 Jul 19;10(7):230402. doi: 10.1098/rsos.230402. PMID: 37476510; PMCID: PMC10354475.

Deshpande SS, Smith GA, van Drongelen W. Third-order motifs are sufficient to fully and uniquely characterize spatiotemporal neural network activity. Sci Rep. 2023 Jan 5;13(1):238. doi: 10.1038/s41598-022-27188-6. PMID: 36604489; PMCID: PMC9816122.

DiRisio GF, Ra Y, Qiu Y, Anzai A, DeAngelis GC. Neurons in Primate Area MSTd Signal Eye Movement Direction Inferred from Dynamic Perspective Cues in Optic Flow. J Neurosci. 2023 Mar 15;43(11):1888-1904. doi: 10.1523/JNEUROSCI.1885-22.2023. Epub 2023 Feb 1. PMID: 36725323; PMCID: PMC10027048.

Freeman JQ, Sheade J, Zhao F, Olopade OI, Nanda R, Huo D. Demographic and Clinical Characteristics Associated With Familiarity, Interest, and Use of Integrative Therapies Among Patients With Breast Cancer. Integr Cancer Ther. 2023 Jan-Dec;22:15347354231185122. doi: 10.1177/15347354231185122. PMID: 37462224; PMCID: PMC10357060.

Lee V, Rodriguez DM, Ganci NK, Zeng S, Ai J, Chao JL, Walker MT, Miller CH, Klawon DEJ, Schoenbach MH, Kennedy DE, Maienschein-Cline M, Socci ND, Clark MR, Savage PA. The endogenous repertoire harbors self-reactive CD4+ T cell clones that adopt a follicular helper T cell-like phenotype at steady state. Nat Immunol. 2023 Mar;24(3):487-500. doi: 10.1038/s41590-023-01425-0. Epub 2023 Feb 9. PMID: 36759711; PMCID: PMC9992328.

Chen L, Zhang LS, Ye C, Zhou H, Liu B, Gao B, Deng Z, Zhao C, He C, Dickinson BC. Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2'-O-methylation. Cell Res. 2023 Jun 15. doi: 10.1038/s41422-023-00836-w. Epub ahead of print. PMID: 37316584.

Dou X, Huang L, Xiao Y, Liu C, Li Y, Zhang X, Yu L, Zhao R, Yang L, Chen C, Yu X, Gao B, Qi M, Gao Y, Shen B, Sun S, He C, Liu J. METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity. Protein Cell. 2023 Feb 23:pwad009. doi: 10.1093/procel/pwad009. Epub ahead of print. PMID: 37030005.

Yu F, Zhu AC, Liu S, Gao B, Wang Y, Khudaverdyan N, Yu C, Wu Q, Jiang Y, Song J, Jin L, He C, Qian Z. RBM33 is a unique m6A RNA-binding protein that regulates ALKBH5 demethylase activity and substrate selectivity. Mol Cell. 2023 Jun 15;83(12):2003-2019.e6. doi: 10.1016/j.molcel.2023.05.010. Epub 2023 May 30. PMID: 37257451; PMCID: PMC10330838.

Shaw DG, Aguirre-Gamboa R, Vieira MC, Gona S, DiNardi N, Wang A, Dumaine A, Gelderloos-Arends J, Earley ZM, Meckel KR, Ciszewski C, Castillo A, Monroe K, Torres J, Shah SC, Colombel JF, Itzkowitz S, Newberry R, Cohen RD, Rubin DT, Quince C, Cobey S, Jonkers IH, Weber CR, Pekow J, Wilson PC, Barreiro LB, Jabri B. Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis. Nat Med. 2023 Jun;29(6):1520-1529. doi: 10.1038/s41591-023-02372-x. Epub 2023 Jun 15. PMID: 37322120; PMCID: PMC10287559.

Hehmeyer J, Spitz F, Marlow H. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies. Curr Opin Genet Dev. 2023 Jun 28;81:102064. doi: 10.1016/j.gde.2023.102064. Epub ahead of print. PMID: 37390583.

Dolezal JM, Wolk R, Hieromnimon HM, Howard FM, Srisuwananukorn A, Karpeyev D, Ramesh S, Kochanny S, Kwon JW, Agni M, Simon RC, Desai C, Kherallah R, Nguyen TD, Schulte JJ, Cole K, Khramtsova G, Garassino MC, Husain AN, Li H, Grossman R, Cipriani NA, Pearson AT. Deep learning generates synthetic cancer histology for explainability and education. NPJ Precis Oncol. 2023 May 29;7(1):49. doi: 10.1038/s41698-023-00399-4. PMID: 37248379; PMCID: PMC10227067.

Chaudagar K, Hieromnimon HM, Khurana R, Labadie B, Hirz T, Mei S, Hasan R, Shafran J, Kelley A, Apostolov E, Al-Eryani G, Harvey K, Rameshbabu S, Loyd M, Bynoe K, Drovetsky C, Solanki A, Markiewicz E, Zamora M, Fan X, Schürer S, Swarbrick A, Sykes DB, Patnaik A. Reversal of Lactate and PD-1-mediated Macrophage Immunosuppression Controls Growth of PTEN/p53-deficient Prostate Cancer. Clin Cancer Res. 2023 May 15;29(10):1952-1968. doi: 10.1158/1078-0432.CCR-22-3350. PMID: 36862086; PMCID: PMC10192075.

Li Y, Smith JJ, Marques F, Osuma A, Huang HC, Kratsios P. Cell context-dependent CFI-1/ARID3 functions control neuronal terminal differentiation. Cell Rep. 2023 Mar 28;42(3):112220. doi: 10.1016/j.celrep.2023.112220. Epub 2023 Mar 9. PMID: 36897776; PMCID: PMC10124151.

Jain N, Richter F, Adzhubei I, Sharp AJ, Gelb BD. Small open reading frames: a comparative genetics approach to validation. BMC Genomics. 2023 May 1;24(1):226. doi: 10.1186/s12864-023-09311-7. PMID: 37127568; PMCID: PMC10152738.

Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One. 2023 Jan 3;18(1):e0274716. doi: 10.1371/journal.pone.0274716. PMID: 36595500; PMCID: PMC9810180.

Kettenburg G. Digest: Salamanders reveal novel trajectories of amphibian MHC evolution. Evolution. 2023 Apr 1;77(4):1165-1166. doi: 10.1093/evolut/qpad033. PMID: 36812053.

Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, and Brook CE. Full genome Nobecovirus sequences from Malagasy fruit bats define a unique evolutionary history for this coronavirus clade. Frontiers in Public health. doi: https://doi.org/10.3389/fpubh.2022.786060  

Jacqueline Corry, Gwenddolen Kettenburg, Amit. A Upadhyay, Megan Wallace, Michelle M. Marti, Elizabeth R. Wonderlich, Stephanie J. Bissel, Kyndal Goss, Timothy J. Sturgeon, Simon C. Watkins, Douglas S. Reed, Steven E. Bosinger, Simon Barratt-Boyes. Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive lethality in nonhuman primates. PLoS Pathogens. doi: 10.1371/journal.ppat.1010395   

Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA 2nd, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn. 2023 Mar;25(3):143-155. doi: 10.1016/j.jmoldx.2022.12.003. PMID: 36828596.

Gao G, Fiorica PN, McClellan J, Barbeira AN, Li JL, Olopade OI, Im HK, Huo D. A joint transcriptome-wide association study across multiple tissues identifies candidate breast cancer susceptibility genes. Am J Hum Genet. 2023 Jun 1;110(6):950-962. doi: 10.1016/j.ajhg.2023.04.005. Epub 2023 May 9. PMID: 37164006; PMCID: PMC10257003.

Ross CF, Laurence-Chasen JD, Li P, Orsbon C, Hatsopoulos NG. Biomechanical and Cortical Control of Tongue Movements During Chewing and Swallowing. Dysphagia. 2023 Jun 16. doi: 10.1007/s00455-023-10596-9. Epub ahead of print. PMID: 37326668.

Earley ZM, Lisicka W, Sifakis JJ, Aguirre-Gamboa R, Kowalczyk A, Barlow JT, Shaw DG, Discepolo V, Tan IL, Gona S, Ernest JD, Matzinger P, Barreiro LB, Morgun A, Bendelac A, Ismagilov RF, Shulzhenko N, Riesenfeld SJ, Jabri B. GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology. Immunity. 2023 Jan 10;56(1):43-57.e10. doi: 10.1016/j.immuni.2022.12.009. PMID: 36630917; PMCID: PMC10262782.

Liu S, Morin SB, Bourand NM, DeClue IL, Delgado GE, Fan J, Foster SK, Imam MS, Johnston CB, Joseph FB, Lu Y, Sehrawat U, Su LC, Tavan K, Zhang KL, Zhang X, Saulsberry L, Gibbons RD. Social Vulnerability and Risk of Suicide in US Adults, 2016-2020. JAMA Netw Open. 2023 Apr 3;6(4):e239995. doi: 10.1001/jamanetworkopen.2023.9995. PMID: 37099296; PMCID: PMC10134005.

Oliva M, Demanelis K, Lu Y, Chernoff M, Jasmine F, Ahsan H, Kibriya MG, Chen LS, Pierce BL. DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. Nat Genet. 2023 Jan;55(1):112-122. doi: 10.1038/s41588-022-01248-z. Epub 2022 Dec 12. PMID: 36510025; PMCID: PMC10249665.

Lungstrom LL, Fedder Z. Digest: Multiple selective pressures drive color diversity in moths. Evolution. 2023 Mar 1;77(3):928-929. doi: 10.1093/evolut/qpad003. Erratum in: Evolution. 2023 Jun 29;77(7):1735. PMID: 36633269.

Falk MJ, Wu J, Matthews A, Sachdeva V, Pashine N, Gardel ML, Nagel SR, Murugan A. Learning to learn by using nonequilibrium training protocols for adaptable materials. Proc Natl Acad Sci U S A. 2023 Jul 4;120(27):e2219558120. doi: 10.1073/pnas.2219558120. Epub 2023 Jun 26. PMID: 37364104; PMCID: PMC10319023.

Destain H, Prahlad M, Kratsios P. Maintenance of neuronal identity in C. elegans and beyond: Lessons from transcription and chromatin factors. Semin Cell Dev Biol. 2023 Jul 11:S1084-9521(23)00140-4. doi: 10.1016/j.semcdb.2023.07.001. Epub ahead of print. PMID: 37438210.

Sefah N, Ndebele S, Prince L, Korasare E, Agbleke M, Nkansah A, Thompson H, Al-Hendy A, Agbleke AA. Uterine fibroids - Causes, impact, treatment, and lens to the African perspective. Front Pharmacol. 2023 Jan 10;13:1045783. doi: 10.3389/fphar.2022.1045783. PMID: 36703761; PMCID: PMC9871264.

Randolph HE, Aguirre-Gamboa R, Locher V, Brunet-Ratnasingham E, Nakanishi T, Richards BJ, Kaufmann DE, Barreiro LB. Common genetic variants modulate the immune response to SARS-CoV-2 infection in a cell state-dependent manner. 2023.

Brunet-Ratnasingham E*, Morin S*, Randolph HE*, Labrecque M, Bélair J, Lima-Barbosa R, Pagliuzza A, Marchitto L, et al. Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific adaptive immunity in patients hospitalized for COVID-19. 2023. Submitted to Nature Immunology.

Rhoda DP, Haber A, Angielczyk KD. Diversification of the ruminant skull along an evolutionary line of least resistance. Sci Adv. 2023 Mar;9(9):eade8929. doi: 10.1126/sciadv.ade8929. Epub 2023 Mar 1. PMID: 36857459; PMCID: PMC9977183.

Li Z, Rasic M, Kwan M, Sepulveda M, McIntosh C, Shastry V, Chen L, Finn P, Perkins D, Alegre ML. Oral administration of the commensal Alistipes onderdonkii prolongs allograft survival. Am J Transplant. 2023 Feb;23(2):272-277. doi: 10.1016/j.ajt.2022.11.011. Epub 2023 Jan 12. PMID: 36804134; PMCID: PMC10041932.

Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biol Evol. 2023 May 12;15(5):evad081. doi: 10.1093/gbe/evad081. Epub ahead of print. PMID: 37170918; PMCID: PMC10210621.

Hage S, Hagan M, Bi D, Stadnik A, Lee J, Romanos S, Srinath A, Shenkar R, Lee C, Horowitz PM, Girard R, Awad IA. Impact of socioeconomics and race on clinical follow-up and trial enrollment and adherence in cerebral cavernous malformation. J Stroke Cerebrovasc Dis. 2023 Jul;32(7):107167. doi: 10.1016/j.jstrokecerebrovasdis.2023.107167. Epub 2023 May 3. PMID: 37146402; PMCID: PMC10201538.

Romanos SG, Srinath A, Li Y, Xie B, Chen C, Li Y, Moore T, Bi D, Sone JY, Lightle R, Hobson N, Zhang D, Koskimäki J, Shen L, McCurdy S, Lai CC, Stadnik A, Piedad K, Carrión-Penagos J, Shkoukani A, Snellings D, Shenkar R, Sulakhe D, Ji Y, Lopez-Ramirez MA, Kahn ML, Marchuk DA, Ginsberg MH, Girard R, Awad IA. Circulating Plasma miRNA Homologs in Mice and Humans Reflect Familial Cerebral Cavernous Malformation Disease. Transl Stroke Res. 2023 Aug;14(4):513-529. doi: 10.1007/s12975-022-01050-3. Epub 2022 Jun 17. PMID: 35715588; PMCID: PMC9758276.

Ben-Oren Y, Strassberg SS, Hovers E, Kolodny O, Creanza N. Modelling effects of inter-group contact on links between population size and cultural complexity. Biol Lett. 2023 Apr;19(4):20230020. doi: 10.1098/rsbl.2023.0020. Epub 2023 Apr 19. PMID: 37073524; PMCID: PMC10114029.

Pernet E, Sun S, Sarden N, Gona S, Nguyen A, Khan N, Mawhinney M, Tran KA, Chronopoulos J, Amberkar D, Sadeghi M, Grant A, Wali S, Prevel R, Ding J, Martin JG, Thanabalasuriar A, Yipp BG, Barreiro LB, Divangahi M. Neonatal imprinting of alveolar macrophages via neutrophil-derived 12-HETE. Nature. 2023 Feb;614(7948):530-538. doi: 10.1038/s41586-022-05660-7. Epub 2023 Jan 4. PMID: 36599368; PMCID: PMC9945843.

Chan SF, Rubenstein DR, Chen IC, Fan YM, Tsai HY, Zheng YW, Shen SF. Higher temperature variability in deforested mountain regions impacts the competitive advantage of nocturnal species. Proc Biol Sci. 2023 May 31;290(1999):20230529. doi: 10.1098/rspb.2023.0529. Epub 2023 May 24. PMID: 37221845; PMCID: PMC10206452.

Hansen GT, Sobreira DR, Weber ZT, Thornburg AG, Aneas I, Zhang L, Sakabe NJ, Joslin AC, Haddad GA, Strobel SM, Laber S, Sultana F, Sahebdel F, Khan K, Li YI, Claussnitzer M, Ye L, Battaglino RA, Nóbrega MA. Genetics of sexually dimorphic adipose distribution in humans. Nat Genet. 2023 Mar;55(3):461-470. doi: 10.1038/s41588-023-01306-0. Epub 2023 Feb 16. PMID: 36797366.

Chandra S, Di Meco A, Dodiya HB, Popovic J, Cuddy LK, Weigle IQ, Zhang X, Sadleir K, Sisodia SS, Vassar R. The gut microbiome regulates astrocyte reaction to Aβ amyloidosis through microglial dependent and independent mechanisms. Mol Neurodegener. 2023 Jul 6;18(1):45. doi: 10.1186/s13024-023-00635-2. PMID: 37415149; PMCID: PMC10324210.

Freeman JQ, Sheade J, Zhao F, Olopade OI, Nanda R, Huo D. Demographic and Clinical Characteristics Associated With Familiarity, Interest, and Use of Integrative Therapies Among Patients With Breast Cancer. Integr Cancer Ther. 2023 Jan-Dec;22:15347354231185122. doi: 10.1177/15347354231185122. PMID: 37462224; PMCID: PMC10357060. 

Miyashita M, Bell JSK, Wenric S, Karaesmen E, Rhead B, Kase M, Kaneva K, De La Vega FM, Zheng Y, Yoshimatsu TF, Khramtsova G, Liu F, Zhao F, Howard FM, Nanda R, Beaubier N, White KP, Huo D, Olopade OI. Molecular profiling of a real-world breast cancer cohort with genetically inferred ancestries reveals actionable tumor biology differences between European ancestry and African ancestry patient populations. Breast Cancer Res. 2023 May 25;25(1):58. doi: 10.1186/s13058-023-01627-2. PMID: 37231433; PMCID: PMC10210411.

Terman E, Sheade J, Zhao F, Howard FM, Jaskowiak N, Tseng J, Chen N, Hahn O, Fleming G, Huo D, Nanda R. The impact of race and age on response to neoadjuvant therapy and long-term outcomes in Black and White women with early-stage breast cancer. Breast Cancer Res Treat. 2023 Jul;200(1):75-83. doi: 10.1007/s10549-023-06943-x. Epub 2023 Apr 29. PMID: 37120458; PMCID: PMC10224832.

Zhao F, Miyashita M, Hattori M, Yoshimatsu T, Howard F, Kaneva K, Jones R, Bell JSK, Fleming GF, Jaskowiak N, Nanda R, Zheng Y, Huo D, Olopade OI. Racial Disparities in Pathological Complete Response Among Patients Receiving Neoadjuvant Chemotherapy for Early-Stage Breast Cancer. JAMA Netw Open. 2023 Mar 1;6(3):e233329. doi: 10.1001/jamanetworkopen.2023.3329. PMID: 36995716; PMCID: PMC10064259.

Shubeck S, Zhao F, Howard FM, Olopade OI, Huo D. Response to Treatment, Racial and Ethnic Disparity, and Survival in Patients With Breast Cancer Undergoing Neoadjuvant Chemotherapy in the US. JAMA Netw Open. 2023 Mar 1;6(3):e235834. doi: 10.1001/jamanetworkopen.2023.5834. PMID: 36995711; PMCID: PMC10064248.

Peiffer DS, Zhao F, Chen N, Hahn OM, Nanda R, Olopade OI, Huo D, Howard FM. Clinicopathologic Characteristics and Prognosis of ERBB2-Low Breast Cancer Among Patients in the National Cancer Database. JAMA Oncol. 2023 Apr 1;9(4):500-510. doi: 10.1001/jamaoncol.2022.7476. PMID: 36821125; PMCID: PMC9951099.