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Shaun Aengus Mahony, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Ariyachet C, Tovaglieri A, Xiang G, Lu J, Shah MS, Richmond CA, Verbeke C, Melton DA, Stanger BZ, Mooney D, Shivdasani RA, Mahony S, Xia Q, Breault DT, Zhou Q. Reprogrammed Stomach Tissue as a Renewable Source of Functional ß Cells for Blood Glucose Regulation. Cell Stem Cell. 2016 Mar 03; 18(3):410-21. PMID: 26908146.
    Citations: 18     Fields:    Translation:AnimalsCells
  2. Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat Neurosci. 2014 Aug; 17(8):1046-54. PMID: 24997765.
    Citations: 28     Fields:    Translation:AnimalsCells
  3. Paik EJ, Mahony S, White RM, Price EN, Dibiase A, Dorjsuren B, Mosimann C, Davidson AJ, Gifford D, Zon LI. A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis. Stem Cell Reports. 2013; 1(5):425-36. PMID: 24286030.
    Citations: 9     Fields:    Translation:Animals
  4. Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI. A multi-parametric flow cytometric assay to analyze DNA-protein interactions. Nucleic Acids Res. 2013 Jan; 41(2):e38. PMID: 23143268.
    Citations:    Fields:    Translation:AnimalsCells
  5. Guo Y, Mahony S, Gifford DK. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol. 2012; 8(8):e1002638. PMID: 22912568.
    Citations: 69     Fields:    Translation:HumansCells
  6. Mazzoni EO, Mahony S, Iacovino M, Morrison CA, Mountoufaris G, Closser M, Whyte WA, Young RA, Kyba M, Gifford DK, Wichterle H. Embryonic stem cell-based mapping of developmental transcriptional programs. Nat Methods. 2011 Nov 13; 8(12):1056-8. PMID: 22081127.
    Citations: 31     Fields:    Translation:AnimalsCells
  7. Zinman G, Brower-Sinning R, Emeche CH, Ernst J, Huang GT, Mahony S, Myers AJ, O'Dee DM, Flynn JL, Nau GJ, Ross TM, Salter RD, Benos PV, Bar Joseph Z, Morel PA. Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One. 2011; 6(7):e22401. PMID: 21789257.
    Citations: 10     Fields:    Translation:AnimalsCells
  8. Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK. Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol. 2011; 12(1):R2. PMID: 21232103.
    Citations: 43     Fields:    Translation:Cells
  9. Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S. Discovering homotypic binding events at high spatial resolution. Bioinformatics. 2010 Dec 15; 26(24):3028-34. PMID: 20966006.
    Citations: 30     Fields:    Translation:Cells
  10. Jung H, Lacombe J, Mazzoni EO, Liem KF, Grinstein J, Mahony S, Mukhopadhyay D, Gifford DK, Young RA, Anderson KV, Wichterle H, Dasen JS. Global control of motor neuron topography mediated by the repressive actions of a single hox gene. Neuron. 2010 Sep 09; 67(5):781-96. PMID: 20826310.
    Citations: 49     Fields:    Translation:AnimalsCells
  11. Wolf JJ, Dowell RD, Mahony S, Rabani M, Gifford DK, Fink GR. Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast. Genetics. 2010 Jun; 185(2):513-22. PMID: 20382833.
    Citations: 11     Fields:    Translation:Animals
  12. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008 Jan; 36(Database issue):D107-13. PMID: 18006570.
    Citations: 111     Fields:    Translation:HumansAnimalsCells
  13. Mahony S, Auron PE, Benos PV. Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics. 2007 Jul 01; 23(13):i297-304. PMID: 17646310.
    Citations: 16     Fields:    Translation:Cells
  14. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 May 10; 447(7141):167-77. PMID: 17495919.
    Citations: 257     Fields:    Translation:HumansAnimalsCells
  15. Mahony S, Benos PV. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W253-8. PMID: 17478497.
    Citations: 213     Fields:    Translation:HumansAnimalsCells
  16. Mahony S, Auron PE, Benos PV. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol. 2007 Mar 30; 3(3):e61. PMID: 17397256.
    Citations: 65     Fields:    Translation:Cells
  17. Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z. Combined analysis reveals a core set of cycling genes. Genome Biol. 2007; 8(7):R146. PMID: 17650318.
    Citations: 23     Fields:    Translation:HumansAnimals
  18. Mahony S, Corcoran DL, Feingold E, Benos PV. Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Genome Biol. 2007; 8(5):R84. PMID: 17506886.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  19. Mahony S, Benos PV, Smith TJ, Golden A. Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Netw. 2006 Jul-Aug; 19(6-7):950-62. PMID: 16839740.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  20. Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JG, Benos PV, Samollow PB, Speed TP, Graves JA, Miller RD. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol. 2006 Mar; 4(3):e46. PMID: 16435885.
    Citations: 59     Fields:    Translation:HumansAnimalsCells
  21. Mahony S, Golden A, Smith TJ, Benos PV. Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Bioinformatics. 2005 Jun; 21 Suppl 1:i283-91. PMID: 15961468.
    Citations: 21     Fields:    Translation:AnimalsCells
  22. Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS. Transcription factor binding site identification using the self-organizing map. Bioinformatics. 2005 May 01; 21(9):1807-14. PMID: 15647296.
    Citations: 23     Fields:    Translation:AnimalsCells
  23. Mahony S, McInerney JO, Smith TJ, Golden A. Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinformatics. 2004 Mar 05; 5:23. PMID: 15070404.
    Citations: 4     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.