Student Publications

Armingol E, Baghdassarian HM, Lewis NE. "The diversification of methods for studying cell-cell interactions and communication." Nat Rev Genet. 2024. PubMed DOI

Baghdassarian HM, Dimitrov D, Armingol E, Saez-Rodriguez J, Lewis NE. "Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples." Cell Rep Methods. 2024;4(4):100758. PubMed PMC DOI

Boussina A, Shashikumar SP, Malhotra A, Owens RL, El-Kareh R, Longhurst CA, Quintero K, Donahue A, Chan TC, Nemati S, Wardi G. "Impact of a deep learning sepsis prediction model on quality of care and survival." NPJ Digit Med. 2024;7(1):14. PubMed PMC DOI

Dolai A, Soltani S, Smarr B, Das A. "Divergent Circadian Foraging Strategies in Response to Diurnal Predation Versus Persistent Rain in Asian Weaver Ant, Oecophylla smaragdina, Suggest Possible Energetic Trade-offs." J Biol Rhythms. 2024;39(3):295-307. PubMed PMC DOI

Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. "Affinity-optimizing enhancer variants disrupt development." Nature. 2024;626(7997):151-159. PubMed PMC DOI

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

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, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. "Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process." Bioessays. 2024;44(5):e2100252. PubMed PMC 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

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