Student Publications
-
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
-
Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. "A multi-scale map of cell structure fusing protein images and interactions." Nature. 2021;600(7889):536-542. PubMed PMC DOI
-
Shu H, Zhou J, Lian Q, Li H, Zhao D, Zeng J, Ma J. "Modeling gene regulatory networks using neural network architectures." Nat Comput Sci. 2021;1(7):491-501. PubMed 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
-
Zhang Z, Zhou J, Tan P, Pang Y, Rivkin AC, Kirchgessner MA, Williams E, Lee CT, Liu H, Franklin AD, Miyazaki PA, Bartlett A, Aldridge AI, Vu M, Boggeman L, Fitzpatrick C, Nery JR, Castanon RG, Rashid M, Jacobs MW, Ito-Cole T, O'Connor C, Pinto-Duartec A, Dominguez B, Smith JB, Niu SY, Lee KF, Jin X, Mukamel EA, Behrens MM, Ecker JR, Callaway EM. "Epigenomic diversity of cortical projection neurons in the mouse brain." Nature. 2021;598(7879):167-173. PubMed PMC DOI
-
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
-
Castro A, Pyke RM, Zhang X, Thompson WK, Day CP, Alexandrov LB, Zanetti M, Carter H. "Strength of immune selection in tumors varies with sex and age." Nat Commun. 2020;11(1):4128. PubMed PMC DOI
-
Dosset M, Castro A, Carter H, Zanetti M. "Telomerase and CD4 T Cell Immunity in Cancer." Cancers (Basel). 2020;12(6). PubMed PMC DOI