Austin Gillen, PhD
Assistant Research Professor, Medicine-Hematology

Publications

• Islam N, Reuben JS, Dale J, Gutman J, McMahon CM, Amaya M, Goodman B, Toninato J, Gasparetto M, Stevens B, Pei S, Gillen A, Staggs S, Engel K, Davis S, Hull M, Burke E, Larchick L, Zane R, Weller G, Jordan C, Smith C. Machine Learning-Based Exploratory Clinical Decision Support for Newly Diagnosed Patients With Acute Myeloid Leukemia Treated With 7 3 Type Chemotherapy or Venetoclax/Azacitidine. JCO Clin Cancer Inform. 2022 Sep;6:e2200030. PubMed PMID: 36194842
• Lee S, Chen YC, Gillen AE, Taliaferro JM, Deplancke B, Li H, Lai EC. Diverse cell-specific patterns of alternative polyadenylation in Drosophila. Nat Commun. 2022 Sep 13;13(1):5372. PubMed PMID: 36100597
• Campbell NV, Mickael C, Kumar S, Zhang H, Campbell IL, Gillen AE, Trentin CO, Diener K, Gao B, Kheyfets VO, Gu S, Kumar R, Phang T, Brown RD, Graham BB, Stenmark KR. Single-cell RNA sequencing and binary hierarchical clustering define lung interstitial macrophage heterogeneity in response to hypoxia. Am J Physiol Lung Cell Mol Physiol. 2022 Jul 1;323(1):L58-L68. PubMed PMID: 35608266
• Fu R, Riemondy KA, Sheridan RM, Hesselberth JR, Jordan CT, Gillen AE. scraps: an end-to-end pipeline for measuring alternative polyadenylation at high resolution using single-cell RNA-seq. Version: 1. bioRxiv [preprint]. 2022 August. 2022.08.22.504859. doi: 10.1101/2022.08.22.504859
• Ransom MR, Engel KL, Stevens BM, Jordan CT, Gillen AE. MuVEH and mitoMuVEH improve discovery of genetic variation from single cells. Version: 1. bioRxiv [preprint]. 2022 November. 2022.11.22.517553. doi: 10.1101/2022.11.22.517553
• Scalzo RL, Foright RM, Hull SE, Knaub LA, Johnson-Murguia S, Kinanee F, Kaplan J, Houck JA, Johnson G, Sharp RR, Gillen AE, Jones KL, Zhang AMY, Johnson JD, MacLean PS, Reusch JEB, Wright-Hobart S, Wellberg EA. Breast Cancer Endocrine Therapy Promotes Weight Gain With Distinct Adipose Tissue Effects in Lean and Obese Female Mice. Endocrinology. 2021 Nov 1;162(11). PubMed PMID: 34410380
• Gillen AE, Goering R, Taliaferro JM. Quantifying alternative polyadenylation in RNAseq data with LABRAT. Methods Enzymol. 2021;655:245-263. PubMed PMID: 34183124
• Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM. LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival. BMC Genomics. 2021 Jun 26;22(1):476. PubMed PMID: 34174817
• Gillen AE, Fu R, Riemondy KA, Jager J, Fang B, Lazar MA, Martin SL. Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability. Front Physiol. 2021;12:662132. PubMed PMID: 34093224
• Mitchell JM, Sucharov J, Pulvino AT, Brooks EP, Gillen AE, Nichols JT. The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing. Development. 2021 Apr 1;148(7). PubMed PMID: 33741714
• Burchill MA, Finlon JM, Goldberg AR, Gillen AE, Dahms PA, McMahan RH, Tye A, Winter AB, Reisz JA, Bohrnsen E, Schafer JB, D'Alessandro A, Orlicky DJ, Kriss MS, Rosen HR, McCullough RL, Jirón Tamburini BA. Oxidized Low-Density Lipoprotein Drives Dysfunction of the Liver Lymphatic System. Cell Mol Gastroenterol Hepatol. 2021;11(2):573-595. PubMed PMID: 32961356
• Burchill MA, Finlon JM, Goldberg AR, Gillen AE, Dahms PA, McMahan RH, Tye A, Winter AB, Reisz JA, Bohrnsen E, Schafer JB, D'Alessandro A, Orlicky DJ, Kriss MS, Rosen HR, McCullough RL, Jirón Tamburini BA. Oxidized Low-Density Lipoprotein Drives Dysfunction of the Liver Lymphatic System. Cell Mol Gastroenterol Hepatol. 2020 Sep 19;11(2):573-595. [Epub ahead of print] PubMed PMID: 32961356
• Brechbuhl HM, Vinod-Paul K, Gillen AE, Kopin EG, Gibney K, Elias AD, Hayashi M, Sartorius CA, Kabos P. Analysis of circulating breast cancer cell heterogeneity and interactions with peripheral blood mononuclear cells. Mol Carcinog. 2020 Oct;59(10):1129-1139. PubMed PMID: 32822091
• Gillen AE, Riemondy KA, Amani V, Griesinger AM, Gilani A, Venkataraman S, Madhavan K, Prince E, Sanford B, Hankinson TC, Handler MH, Vibhakar R, Jones KL, Mitra S, Hesselberth JR, Foreman NK, Donson AM. Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology. Cell Rep. 2020 Aug 11;32(6):108023. PubMed PMID: 32783945
• Fu R, Gillen AE, Sheridan RM, Tian C, Daya M, Hao Y, Hesselberth JR, Riemondy KA. clustifyr: an R package for automated single-cell RNA sequencing cluster classification. F1000Res. 2020;9:223. PubMed PMID: 32765839
• Brechbuhl HM, Barrett AS, Kopin E, Hagen JC, Han AL, Gillen AE, Finlay-Schultz J, Cittelly DM, Owens P, Horwitz KB, Sartorius CA, Hansen K, Kabos P. Fibroblast subtypes define a metastatic matrisome in breast cancer. JCI Insight. 2020 Feb 27;5(4). PubMed PMID: 32045383
• Pei S, Pollyea DA, Gustafson A, Stevens BM, Minhajuddin M, Fu R, Riemondy KA, Gillen AE, Sheridan RM, Kim J, Costello JC, Amaya ML, Inguva A, Winters A, Ye H, Krug A, Jones CL, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers JR, Ashton JM, Nemkov T, D'Alessandro A, Gutman JA, Ramsey HE, Savona MR, Smith CA, Jordan CT. Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Patients with Acute Myeloid Leukemia. Cancer Discov. 2020 Apr;10(4):536-551. PubMed PMID: 31974170
• Yang W, Trahan GD, Howell ED, Speck NA, Jones KL, Gillen AE, Riemondy K, Hesselberth J, Bryder D, Ernst P. Enhancing Hematopoiesis from Murine Embryonic Stem Cells through MLL1-Induced Activation of a Rac/Rho/Integrin Signaling Axis. Stem Cell Reports. 2020 Feb 11;14(2):285-299. PubMed PMID: 31951812
• Stevens BM, Jones CL, Pollyea DA, Culp-Hill R, D’Alessandro A, Winters A, Krug A, Abbott D, Goosman M, Pei S, Ye H, Gillen AE, Becker MW, Savona MR, SmithC C, Jordan CT. Fatty acid metabolism underlies venetoclax resistance in acute myeloid leukemia stem cells. Nat Cancer 1, 1176–1187 (2020). https://doi.org/10.1038/s43018-020-00126-z
• Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM. LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival. bioRxiv 2020.10.05.326702; doi: https://doi.org/10.1101/2020.10.05.326702
• Fu R, Gillen AE, Grabek KR, Riemondy KA, Epperson LE, Bustamante CD, Hesselberth JR, Martin SL. Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal. Front Physiol. 2020;11:624677. PubMed PMID: 33536943