Student Publications

Begzati A, Godinez-Macias KP, Long T, Watrous JD, Moranchel R, Kantz ED, Tuomilehto J, Havulinna AS, Niiranen TJ, Jousilahti P, Salomaa V, Yu B, Norby F, Rebholz CM, Selvin E, Winzeler EA, Cheng S, Alotaibi M, Goyal R, Ideker T, Jain M, Majithia AR. "Plasma Lipid Metabolites, Clinical Glycemic Predictors, and Incident Type 2 Diabetes." Diabetes Care. 2025;48(3):473-480. PubMed PMC DOI

Ferry A, Mempel KM, Monell A, Reina-Campos M, Scharping NE, Heeg M, Takehara KK, Schokrpur S, Kuo N, Saddawi-Konefka R, Gutkind JS, Goldrath AW. "The XCL1-XCR1 axis supports intestinal tissue residency and antitumor immunity." J Exp Med. 2025;222(2). PubMed PMC DOI

Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Godoy Magalhaes L, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean KJ, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. "Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining." NPJ Drug Discov. 2025;2(1):3. PubMed PMC DOI

Nobori T, Monell A, Lee TA, Sakata Y, Shirahama S, Zhou J, Nery JR, Mine A, Ecker JR. "A rare PRIMER cell state in plant immunity." Nature. 2025;638(8049):197-205. PubMed PMC DOI

Reina-Campos M, Monell A, Ferry A, Luna V, Cheung KP, Galletti G, Scharping NE, Takehara KK, Quon S, Challita PP, Boland B, Lin YH, Wong WH, Indralingam CS, Neadeau H, Alarcón S, Yeo GW, Chang JT, Heeg M, Goldrath AW. "Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted." Nature. 2025;639(8054):483-492. PubMed PMC DOI

Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. "State of the interactomes: an evaluation of molecular networks for generating biological insights." Mol Syst Biol. 2025;21(1):1-29. PubMed PMC DOI

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

Godinez-Macias KP, Winzeler EA. "CACTI: an in silico chemical analysis tool through the integration of chemogenomic data and clustering analysis." J Cheminform. 2024;16(1):84. PubMed PMC DOI

Jiang T, Godinez-Macias KP, Collins JE, Lee JW, Wendt KL, Carolino K, Chakrabarti D, Cichewicz RH, Winzeler EA. "Identification of fungal natural products with potent inhibition in Toxoplasma gondii." Microbiol Spectr. 2024;12(4):e0414223. 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

Luth MR, Godinez-Macias KP, Chen D, Okombo J, Thathy V, Cheng X, Daggupati S, Davies H, Dhingra SK, Economy JM, Edgar RCS, Gomez-Lorenzo MG, Istvan ES, Jado JC, LaMonte GM, Melillo B, Mok S, Narwal SK, Ndiaye T, Ottilie S, Palomo Diaz S, Park H, Peña S, Rocamora F, Sakata-Kato T, Small-Saunders JL, Summers RL, Tumwebaze PK, Vanaerschot M, Xia G, Yeo T, You A, Gamo FJ, Goldberg DE, Lee MCS, McNamara CW, Ndiaye D, Rosenthal PJ, Schreiber SL, Serra G, De Siqueira-Neto JL, Skinner-Adams TS, Uhlemann AC, Kato N, Lukens AK, Wirth DF, Fidock DA, Winzeler EA. "Systematic in vitro evolution in Plasmodium falciparum reveals key determinants of drug resistance." Science. 2024;386(6725):eadk9893. 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

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, 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