Student Publications

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

Lorenz DA, Her HL, Shen KA, Rothamel K, Hutt KR, Nojadera AC, Bruns SC, Manakov SA, Yee BA, Chapman KB, Yeo GW. "Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP." Nat Methods. 2023;20(1):65-69. PubMed PMC DOI

Massarat AR, Lamkin M, Reeve C, Williams AL, D'Antonio M, Gymrek M. "Haptools: a toolkit for admixture and haplotype analysis." Bioinformatics. 2023;39(3). PubMed PMC DOI

Mittal N, Davis C, McLean P, Calla J, Godinez-Macias KP, Gardner A, Healey D, Orjuela-Sanchez P, Ottilie S, Chong Y, Gibson C, Winzeler EA. "Human nuclear hormone receptor activity contributes to malaria parasite liver stage development." Cell Chem Biol. 2023;30(5):486-498.e7. PubMed PMC DOI

Rogers P, Boussina AE, Shashikumar SP, Wardi G, Longhurst CA, Nemati S. "Optimizing the Implementation of Clinical Predictive Models to Minimize National Costs: Sepsis Case Study." J Med Internet Res. 2023;25:e43486. PubMed PMC DOI

Rosenthal SB, Wright SN, Liu S, Churas C, Chilin-Fuentes D, Chen CH, Fisch KM, Pratt D, Kreisberg JF, Ideker T. "Mapping the common gene networks that underlie related diseases." Nat Protoc. 2023;18(6):1745-1759. PubMed PMC DOI

Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. "Diverse logics and grammar encode notochord enhancers." Cell Rep. 2023;42(2):112052. PubMed DOI

Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li YE, Siletti K, Liem M, Claffey N, O'Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. "Single-cell DNA methylation and 3D genome architecture in the human brain." Science. 2023;382(6667):eadf5357. PubMed PMC DOI

Vo D, Ghosh P, Sahoo D. "Artificial intelligence-guided discovery of gastric cancer continuum." Gastric Cancer. 2023;26(2):286-297. PubMed PMC DOI

Wen X, Zhong S. "Alu transposable elements rewire enhancer-promoter network through RNA pairing." Mol Cell. 2023;83(18):3234-3235. PubMed DOI

Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. "Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks." Cell Rep. 2023;42(8):112873. PubMed PMC DOI

Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. "Conserved and divergent gene regulatory programs of the mammalian neocortex." Nature. 2023;624(7991):390-402. PubMed PMC DOI

Zhou J, Zhang Z, Wu M, Liu H, Pang Y, Bartlett A, Peng Z, Ding W, Rivkin A, Lagos WN, Williams E, Lee CT, Miyazaki PA, Aldridge A, Zeng Q, Salinda JLA, Claffey N, Liem M, Fitzpatrick C, Boggeman L, Yao Z, Smith KA, Tasic B, Altshul J, Kenworthy MA, Valadon C, Nery JR, Castanon RG, Patne NS, Vu M, Rashid M, Jacobs M, Ito T, Osteen J, Emerson N, Lee J, Cho S, Rink J, Huang HH, Pinto-Duartec A, Dominguez B, Smith JB, O'Connor C, Zeng H, Chen S, Lee KF, Mukamel EA, Jin X, Margarita Behrens M, Ecker JR, Callaway EM. "Brain-wide correspondence of neuronal epigenomics and distant projections." Nature. 2023;624(7991):355-365. PubMed PMC DOI