Student Publications

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

Castro A, Ozturk K, Zanetti M, Carter H. "In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses." PLoS One. 2021;16(2):e0246731. PubMed PMC DOI

Castro A, Zanetti M, Carter H. "Neoantigen Controversies." Annu Rev Biomed Data Sci. 2021;4. DOI

Chiang AWT, Baghdassarian HM, Kellman BP, Bao B, Sorrentino JT, Liang C, Kuo CC, Masson HO, Lewis NE. "Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy." J Biomed Sci. 2021;28(1):50. PubMed PMC DOI

Dehkordi SR, Luebeck J, Bafna V. "FaNDOM: Fast nested distance-based seeding of optical maps." Patterns. 2021;2:100248. PubMed PMC DOI

Ding B, Liu Y, Liu Z, Zheng L, Xu P, Chen Z, Wu P, Zhao Y, Pan Q, Guo Y, Wei W, Wang W. "Noncoding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability." Sci Adv. 2021;7(45):eabi6020. 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

Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. "Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma." Microorganisms. 2021;9(10). PubMed PMC DOI

Hasenstab KA, Yuan N, Retson T, Conrad DJ, Kligerman S, Lynch DA, Hsiao A. "Automated CT Staging of Chronic Obstructive Pulmonary Disease Severity for Predicting Disease Progression and Mortality with a Deep Learning Convolutional Neural Network." Radiol Cardiothorac Imaging. 2021;3(2):e200477. PubMed PMC DOI

Her HL, Lin PT, Wu YW. "PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains." BMC Bioinformatics. 2021;22(1):548. 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

Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. "ecDNA hubs drive cooperative intermolecular oncogene expression." Nature. 2021;600(7890):731-736. 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

Kuo CC, Chiang AWT, Baghdassarian HM, Lewis NE. "Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation." Cell Syst. 2021;12(9):873-884.e4. PubMed PMC DOI

Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, Poirion OB, Preissl S, Pinto-Duarte A, O'Connor C, Boggeman L, Fitzpatrick C, Nunn M, Mukamel EA, Zhang Z, Callaway EM, Ren B, Dixon JR, Behrens MM, Ecker JR. "DNA methylation atlas of the mouse brain at single-cell resolution." Nature. 2021;598(7879):120-128. 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

Moshiri N. "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics. 2021;37(5):714-716. PubMed DOI

Moshiri N, Smith DM, Mirarab S. "HIV Care Prioritization Using Phylogenetic Branch Length." J Acquir Immune Defic Syndr. 2021;86(5):626-637. PubMed PMC DOI

Pang J, Nguyen N, Luebeck J, Ball L, Finegersh A, Ren S, Nakagawa T, Flagg M, Sadat S, Mischel PS, Xu G, Fisch K, Guo T, Cahill G, Panuganti B, Bafna V, Califano J. "Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription." Clin Cancer Res. 2021;27(24):6772-6786. PubMed PMC DOI

Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. "Timing the SARS-CoV-2 index case in Hubei province." Science. 2021;372(6540):412-417. PubMed PMC DOI