Training Grant Publications

2022

Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli AE. "Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms." Nucleic Acids Res. 2022;50(8):4685-4702. PubMed PMC DOI
Soncin F, Morey R, Bui T, Requena DF, Cheung VC, Kallol S, Kittle R, Jackson MG, Farah O, Chousal J, Meads M, Pizzo D, Horii M, Fisch KM, Parast MM. "Derivation of functional trophoblast stem cells from primed human pluripotent stem cells." Stem Cell Reports. 2022;17(6):1303-1317. PubMed PMC DOI
Sorrentino JT, Golden GJ, Morris C, Painter CD, Nizet V, Campos AR, Smith JW, Karlsson C, Malmström J, Lewis NE, Esko JD, Gómez Toledo A. "Vascular Proteome Responses Precede Organ Dysfunction in a Murine Model of Staphylococcus aureus Bacteremia." MSystems. 2022;7(4):e0039522. PubMed PMC DOI
Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. "Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain." Cell Res. 2022;32(11):1008-1021. PubMed PMC DOI

2021

Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW. "Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes." Nat Methods. 2021;18(5):507-519. PubMed PMC DOI
Golden GJ, Toledo AG, Marki A, Sorrentino JT, Morris C, Riley RJ, Spliid C, Chen Q, Cornax I, Lewis NE, Varki N, Le D, Malmström J, Karlsson C, Ley K, Nizet V, Esko JD. "Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis." MBio. 2021;12(5):e0118121. PubMed PMC DOI
Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. "A Systems View of the Heparan Sulfate Interactome." J Histochem Cytochem. 2021;69(2):105-119. PubMed PMC DOI
Horii M, Morey R, Bui T, Touma O, Nelson KK, Cho HY, Rishik H, Laurent LC, Parast MM. "Modeling preeclampsia using human induced pluripotent stem cells." Sci Rep. 2021;11(1):5877. PubMed PMC DOI
Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. "Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing." BMC Genomics. 2021;22(1):69. PubMed PMC DOI
Klie A, Tsui BY, Mollah S, Skola D, Dow M, Hsu CN, Carter H. "Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition." Database (Oxford). 2021;2021. PubMed PMC DOI
Massarat AR, Sen A, Jaureguy J, Tyndale ST, Fu Y, Erikson G, McVicker G. "Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq." Nucleic Acids Res. 2021. PubMed DOI
Maurya MR, Gupta S, Li JY, Ajami NE, Chen ZB, Shyy JY, Chien S, Subramaniam S. "Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions." Proc Natl Acad Sci U S A. 2021;118(4). PubMed PMC DOI
Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M. "Patterns of de novo tandem repeat mutations and their role in autism." Nature. 2021;589(7841):246-250. PubMed PMC DOI
Morey R, Farah O, Kallol S, Requena DF, Meads M, Moretto-Zita M, Soncin F, Laurent LC, Parast MM. "Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast." Front Cell Dev Biol. 2021;9:702046. PubMed PMC DOI
Vo DT, Fuller MR, Tindle C, Anandachar MS, Das S, Sahoo D, Ghosh P. "SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia." IScience. 2021;24(10):103121. PubMed PMC DOI

2020

Baxter SL, Klie AR, Radha Saseendrakumar B, Ye GY, Hogarth M. "Text Processing for Detection of Fungal Ocular Involvement in Critical Care Patients: Cross-Sectional Study." J Med Internet Res. 2020;22(8):e18855. PubMed PMC DOI
Baxter SL, Klie AR, Saseendrakumar BR, Ye GY, Hogarth M, Nemati S. "Predicting Mortality in Critical Care Patients with Fungemia Using Structured and Unstructured Data." Annu Int Conf IEEE Eng Med Biol Soc. 2020;2020:5459-5463. PubMed PMC DOI
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. "An atlas of dynamic chromatin landscapes in mouse fetal development." Nature. 2020;583(7818):744-751. PubMed PMC DOI
Hyun JC, Kavvas ES, Monk JM, Palsson BO. "Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens." PLoS Comput Biol. 2020;16(3):e1007608. PubMed PMC DOI
Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H, i2QTL Consortium, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. "Properties of structural variants and short tandem repeats associated with gene expression and complex traits." Nat Commun. 2020;11(1):2927. PubMed PMC DOI
Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. "Mutational profiling of micro-dissected pre-malignant lesions from archived specimens." BMC Med Genomics. 2020;13(1):173. PubMed PMC DOI
Xie X, Shah S, Holtz A, Rose J, Basisty N, Schilling B. "Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization." J Vis Exp. 2020(156). PubMed PMC DOI

2019

Banerjee S, Wei T, Wang J, Lee JJ, Gutierrez HL, Chapman O, Wiley SE, Mayfield JE, Tandon V, Juarez EF, Chavez L, Liang R, Sah RL, Costello C, Mesirov JP, de la Vega L, Cooper KL, Dixon JE, Xiao J, Lei X. "Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression." Proc Natl Acad Sci U S A. 2019;116(49):24881-24891. PubMed PMC DOI
Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. "Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers." Cell. 2019;179(2):373-391.e27. PubMed PMC DOI
D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. "Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease." Elife. 2019;8. PubMed PMC DOI