Student Publications

2023

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
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
Zu S, Li YE, Wang K, Armand EJ, Mamde S, Amaral ML, Wang Y, Chu A, Xie Y, Miller M, Xu J, Wang Z, Zhang K, Jia B, Hou X, Lin L, Yang Q, Lee S, Li B, Kuan S, Liu H, Zhou J, Pinto-Duarte A, Lucero J, Osteen J, Nunn M, Smith KA, Tasic B, Yao Z, Zeng H, Wang Z, Shang J, Behrens MM, Ecker JR, Wang A, Preissl S, Ren B. "Single-cell analysis of chromatin accessibility in the adult mouse brain." Nature. 2023;624(7991):378-389. PubMed PMC DOI

2022

Armingol E, Baghdassarian HM, Martino C, Perez-Lopez A, Aamodt C, Knight R, Lewis NE. "Context-aware deconvolution of cell-cell communication with Tensor-cell2cell." Nat Commun. 2022;13(1):3665. PubMed PMC DOI
Armingol E, Ghaddar A, Joshi CJ, Baghdassarian H, Shamie I, Chan J, Her HL, Berhanu S, Dar A, Rodriguez-Armstrong F, Yang O, O'Rourke EJ, Lewis NE. "Inferring a spatial code of cell-cell interactions across a whole animal body." PLoS Comput Biol. 2022;18(11):e1010715. PubMed PMC DOI
Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. "Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases." MSystems. 2022:e0137821. PubMed DOI
Armstrong G, Rahmn G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R. "Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data." Front Bioinform. 2022;2:821861. DOI
Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. "Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA." Nature. 2022;602(7897):510-517. PubMed PMC DOI
Boeder S, Kobayashi E, Ramesh G, Serences B, Kulasa K, Majithia AR. "Accuracy and Glycemic Efficacy of Continuous Glucose Monitors in Critically Ill COVID-19 Patients: A Retrospective Study." J Diabetes Sci Technol. 2022:1.93E+16. PubMed DOI
Dekel C, Morey R, Hanna J, Laurent LC, Ben-Yosef D, Amir H. "Stabilization of hESCs in two distinct substates along the continuum of pluripotency." IScience. 2022;25(12):105469. PubMed PMC DOI
Ghosh P, Campos VJ, Vo DT, Guccione C, Goheen-Holland V, Tindle C, Mazzini GS, He Y, Alexandrov LB, Lippman SM, Gurski RR, Das S, Yadlapati R, Curtius K, Sahoo D. "AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas." JCI Insight. 2022;7(18). PubMed PMC DOI
Her HL, Boyle E, Yeo GW. "Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites." Bioinform Adv. 2022;2(1):vbac083. PubMed PMC DOI