Student Publications

2024

Mah CK, Ahmed N, Lopez NA, Lam DC, Pong A, Monell A, Kern C, Han Y, Prasad G, Cesnik AJ, Lundberg E, Zhu Q, Carter H, Yeo GW. "Bento: a toolkit for subcellular analysis of spatial transcriptomics data." Genome Biol. 2024;25(1):82. PubMed PMC DOI
Mason AE, Kasl P, Soltani S, Green A, Hartogensis W, Dilchert S, Chowdhary A, Pandya LS, Siwik CJ, Foster SL, Nyer M, Lowry CA, Raison CL, Hecht FM, Smarr BL. "Elevated body temperature is associated with depressive symptoms: results from the TemPredict Study." Sci Rep. 2024;14(1):1884. PubMed PMC DOI
Medina-Munoz HC, Kofman E, Jagannatha P, Boyle EA, Yu T, Jones KL, Mueller JR, Lykins GD, Doudna AT, Park SS, Blue SM, Ranzau BL, Kohli RM, Komor AC, Yeo GW. "Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies." Nat Commun. 2024;15(1):875. PubMed PMC DOI
Pong A, Mah CK, Yeo GW, Lewis NE. "Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment." Curr Opin Biotechnol. 2024;85:103048. PubMed DOI
Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. "Robustness of cancer microbiome signals over a broad range of methodological variation." Oncogene. 2024;43(15):1127-1148. PubMed PMC DOI
Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Charles Richard JL, Zhong S. "Single-cell multiplex chromatin and RNA interactions in ageing human brain." Nature. 2024;628(8008):648-656. PubMed PMC DOI
Zhang K, Zemke NR, Armand EJ, Ren B. "A fast, scalable and versatile tool for analysis of single-cell omics data." Nat Methods. 2024;21(2):217-227. PubMed PMC DOI
Zhang R, Fang J, Xie X, Carrico C, Meyer JG, Wei L, Bons J, Rose J, Riley R, Kwok R, Ashok Kumaar PV, Zhang Y, He W, Nishida Y, Liu X, Locasale JW, Schilling B, Verdin E. "Regulation of urea cycle by reversible high-stoichiometry lysine succinylation." Nat Metab. 2024;6(3):550-566. PubMed DOI

2023

Abe Y, Kofman ER, Almeida M, Ouyang Z, Ponte F, Mueller JR, Cruz-Becerra G, Sakai M, Prohaska TA, Spann NJ, Resende-Coelho A, Seidman JS, Stender JD, Taylor H, Fan W, Link VM, Cobo I, Schlachetzki JCM, Hamakubo T, Jepsen K, Sakai J, Downes M, Evans RM, Yeo GW, Kadonaga JT, Manolagas SC, Rosenfeld MG, Glass CK. "RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression." Mol Cell. 2023;83(19):3421-3437.e11. PubMed PMC DOI
Amrollahi F, Shashikumar SP, Boussina A, Yhdego H, Nayebnazar A, Yung N, Wardi G, Nemati S. "Predicting Hospital Readmission among Patients with Sepsis Using Clinical and Wearable Data." Annu Int Conf IEEE Eng Med Biol Soc. 2023;2023:1-4. PubMed PMC DOI
Boussina A, Shashikumar S, Amrollahi F, Pour H, Hogarth M, Nemati S. "Development & Deployment of a Real-time Healthcare Predictive Analytics Platform." Annu Int Conf IEEE Eng Med Biol Soc. 2023;2023:1-4. PubMed PMC DOI
Boussina A, Wardi G, Shashikumar SP, Malhotra A, Zheng K, Nemati S. "Representation Learning and Spectral Clustering for the Development and External Validation of Dynamic Sepsis Phenotypes: Observational Cohort Study." J Med Internet Res. 2023;25:e45614. PubMed PMC DOI
Bruce LK, Kasl P, Soltani S, Viswanath VK, Hartogensis W, Dilchert S, Hecht FM, Chowdhary A, Anglo C, Pandya L, Dasgupta S, Altintas I, Gupta A, Mason AE, Smarr BL. "Variability of temperature measurements recorded by a wearable device by biological sex." Biol Sex Differ. 2023;14(1):76. PubMed PMC DOI
Bruce LK, Kasl P, Soltani S, Viswanath VK, Hartogensis W, Dilchert S, Hecht FM, Chowdhary A, Anglo C, Pandya L, Dasgupta S, Altintas I, Gupta A, Mason AE, Smarr BL. "Correction: Variability of temperature measurements recorded by a wearable device by biological sex." Biol Sex Differ. 2023;14(1):82. PubMed PMC DOI
Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S. "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells." Nat Commun. 2023;14(1):6519. PubMed PMC DOI
Campos FA, Bruno S, Fu Y, Del Vecchio D, Williams RJ. "Comparison Theorems for Stochastic Chemical Reaction Networks." Bull Math Biol. 2023;85(5):39. PubMed PMC DOI
Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. "Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma." Nat Genet. 2023;55(12):2189-2199. PubMed PMC DOI
Ghaddar A, Armingol E, Huynh C, Gevirtzman L, Lewis NE, Waterston R, O'Rourke EJ. "Whole-body gene expression atlas of an adult metazoan." Sci Adv. 2023;9(25):eadg0506. PubMed PMC DOI
Guccione C, McDonald D, Fielding-Miller R, Curtius K, Knight R. "You are what you excrete." Nat Microbiol. 2023;8(6):1002-1003. PubMed DOI
Horii M, To C, Morey R, Jacobs MB, Li Y, Nelson KK, Meads M, Siegel BA, Pizzo D, Adami R, Zhang-Rutledge K, Lamale-Smith L, Laurent LC, Parast MM. "Histopathologic and Transcriptomic Profiling Identifies Novel Trophoblast Defects in Patients With Preeclampsia and Maternal Vascular Malperfusion." Mod Pathol. 2023;36(2):100035. PubMed PMC DOI
Jia BB, Jussila A, Kern C, Zhu Q, Ren B. "A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH." Nat Biotechnol. 2023. PubMed DOI
Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. "Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development." Dev Cell. 2023;58(21):2206-2216.e5. PubMed PMC DOI
Kathman SG, Koo SJ, Lindsey GL, Her HL, Blue SM, Li H, Jaensch S, Remsberg JR, Ahn K, Yeo GW, Ghosh B, Cravatt BF. "Remodeling oncogenic transcriptomes by small molecules targeting NONO." Nat Chem Biol. 2023. PubMed DOI
Kofman E, Yee B, Medina-Munoz HC, Yeo GW. "FLARE: a fast and flexible workflow for identifying RNA editing foci." BMC Bioinformatics. 2023;24(1):370. PubMed PMC DOI
Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, Osteen JK, Pinto-Duarte A, Lee J, Rink J, Cho S, Emerson N, Nunn M, O'Connor C, Wu Z, Stoica I, Yao Z, Smith KA, Tasic B, Luo C, Dixon JR, Zeng H, Ren B, Behrens MM, Ecker JR. "Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain." Nature. 2023;624(7991):366-377. PubMed PMC DOI