Training Grant Publications

2024

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
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
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

2023

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

2022

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
Hyun JC, Monk JM, Palsson BO. "Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity." BMC Genomics. 2022;23(1):7. PubMed PMC DOI
Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. "FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA." NAR Genom Bioinform. 2022;4(2):lqac032. PubMed PMC DOI
Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. "Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3." Elife. 2022;11. PubMed PMC DOI
Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. "The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ." NPJ Breast Cancer. 2022;8(1):6. PubMed PMC DOI
Nachmanson D, Pagadala M, Steward J, Cheung C, Bruce LK, Lee NQ, O'Keefe TJ, Lin GY, Hasteh F, Morris GP, Carter H, Harismendy O. "Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes." J Transl Med. 2022;20(1):623. PubMed PMC DOI
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