[ * co-first authors; † co-corresponding authors; group members in bold ]

Journal Articles

  1. Deconvolving sequence features that discriminate between overlapping regulatory annotations
    A Kakumanu, S Velasco, EO Mazzoni, S Mahony
    PLoS Computational Biology (2017) 13(10):e1005795
    [Abstract] [Open Access Article]
  2. miniMDS: 3D structural inference from high-resolution Hi-C data
    L Rieber, S Mahony
    Bioinformatics (2017) 33 (14):i261-i266
    [Abstract] [Open Access Article]
  3. A multi-step transcriptional and chromatin state cascade underlies motor neuron programming
    S Velasco*, MM Ibrahim*, A Kakumanu*, G Garipler, B Aydin, MA Al-Sayegh, A Hirsekorn, F Abdul-Rahman, R Satija, U Ohler, S Mahony, EO Mazzoni
    Cell Stem Cell (2017) 20(2):205-217.e8
    [Abstract] [Article]
  4. The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation
    M Iwafuchi-Doi, G Donahue, A Kakumanu, JA Watts, S Mahony, BF Pugh, D Lee, KH Kaestner, KS Zaret
    Molecular Cell (2016) 62(1): 72-91
    [Abstract] [Article]
  5. Engineered stomach tissues as a renewable source of functional beta-cells for blood glucose regulation
    C Ariyachet, A Tovaglieri, G Xiang, J Lu, MS Shah, CA Richmond, C Verbeke, DA Melton, BZ Stanger, D Mooney, RA Shivdasani, S Mahony, Q Xia, DT Breault, Q Zhou
    Cell Stem Cell (2016) 18(3):410-421
    [Abstract] [Article]
  6. Phenome-wide interaction study (PheWIS) in AIDS clinical trials group data (ACTG)
    SS Verma, AT Frase, A Verma, SA Pendergrass, S Mahony, DW Haas, MD Ritchie
    Pacific Symposium on Biocomputing (2016) 21:57-68
    [Abstract] [Open Access Article] [PMC Free Text]
  7. Genome-wide organization of GATA1 and TAL1 determined at high resolution
    GC Han, V Vinayachandran, A Bataille, B Park, KY Chan-Salis, CA Keller, M Long, S Mahony, RC Hardison, BF Pugh
    Molecular & Cell Biology (2016) 36(1):157-172
    [Abstract] [Open Access Article] [PMC Free Text]
  8. Protein-DNA binding in high resolution
    S Mahony, BF Pugh
    Critical Reviews in Biochemistry and Molecular Biology (2015) 4:269-283
    [Abstract] [Article] [PMC Free Text]
  9. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons
    S Lodato, BJ Molyneax, E Zuccaro, LA Goff, H-H Chen, W Yuan, A Meleski, E Takahashi, S Mahony, JL Rinn, DK Gifford, P Arlotta
    Nature Neuroscience (2014) 17(8):1046-54
    [Abstract] [Article] [PMC Free Text]
  10. An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding
    S Mahony*, MD Edwards*, EO Mazzoni, RI Sherwood, A Kakumanu, CA Morrison, H Wichterle, DK Gifford
    PLoS Computational Biology (2014) 10(3):e1003501
    [Abstract] [Open Access Article] [PMC Free Text]
  11. A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis
    EJ Paik, S Mahony, RM White, EN Price, A DiBiase, B Dorjsuren, C Mosimann, AJ Davidson, DK Gifford, LI Zon
    Stem Cell Reports (2013) 1(5):425-436
    [Abstract] [Open Access Article] [PMC Free Text]
  12. Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity
    EO Mazzoni*, S Mahony*, M Closser, CA Morrison, S Nedelec, DJ Williams, D An, DK Gifford, H Wichterle
    Nature Neuroscience (2013) 16(9):1219-1227
    [Abstract] [Article] [PMC Free Text]
  13. Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals
    EO Mazzoni*, S Mahony*, M Peljto*, T Patel, SR Thornton, S McCuine, C Reeder, LA Boyer, RA Young, DK Gifford, H Wichterle
    Nature Neuroscience (2013) 16(9):1191-1198 
    [Abstract] [Article] [PMC Free Text]
  14. A multi-parametric flow cytometric assay to analyze DNA-protein interactions
    M Arbab, S Mahony, H Cho, J Chick, PA Rolfe, J Van Hoff, V Morris, S Gygi, RL Maas, DK Gifford, R Sherwood
    Nucleic Acids Research (2013) 41(2):e38
    [Abstract] [Open Access Article] [PMC Free Text]
  15. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    Y Guo, S Mahony, DK Gifford
    PLoS Computational Biology (2012) 8(8):e1002638
    [Abstract] [Open Access Article] [PMC Free Text]
  16. Embryonic stem cell based system for the discovery and mapping of developmental transcriptional programs
    EO Mazzoni, S Mahony, M Iacovino, CA Morrison, G Mountoufaris, M Closser, WA Whyte, RA Young, M Kyba, DK Gifford, H Wichterle
    Nature Methods (2011) 8(12):1056-1058
    [Abstract] [Article] [PMC Free Text]
  17. Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque
    GE Zinman, R Brower-Sinning, CH Emeche, J Ernst, GT Huang, S Mahony, AJ Myers, DM O’Dee, JL Flynn, GJ Nau, TM Ross, RD Salter, PV Benos, Z Bar-Joseph, PA Morel
    PLoS ONE (2011) 6(7):e22401
    [Abstract] [Open Access Article] [PMC Free Text]
  18. Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
    S Mahony*, EO Mazzoni*, S McCuine, RA Young, H Wichterle, DK Gifford
    Genome Biology (2011) 12(1):R2 
    [Abstract] [Open Access Article] [PMC Free Text]
  19. Discovering homotypic binding events at high spatial resolution
    Y Guo, G Papachristoudis, RC Altshuler, GK Gerber, TS Jaakkola, DK Gifford, S Mahony
    Bioinformatics (2010) 26(24):3028-3034
    [Abstract] [Article] [PMC Free Text]
  20. Global control of motor neuron topography mediated by the repressive actions of a single Hox gene
    H Jung, J Lacombe, EO Mazzoni, KF Leim, J Grinstein, S Mahony, D Mukopadhyay, DK Gifford, RA Young, KV Anderson, H Wichterle, JS Dasen
    Neuron (2010) 67(5):781-796
    [Abstract] [Open Access Article] [PMC Free Text]
  21. Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast
    JJ Wolf, RD Dowell, S Mahony, M Rabani, DK Gifford, GR Fink
    Genetics (2010) 185:513-522
    [Abstract] [Article] [PMC Free Text]
  22. ORegAnno: an open-access community-driven resource for regulatory annotation
    OL Griffith, SB Montgomery, …, S Mahony (7 of 29 authors), …, CM Bergman, SJM Jones
    Nucleic Acids Research (2008) 36(Database issue):D107-13
    [Abstract] [Open Access Article] [PMC Free Text]
  23. Combined analysis reveals a core set of cycling genes
    Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden, Z Bar-Joseph
    Genome Biology (2007) 8(7):R146
    [Abstract] [Open Access Article] [PMC Free Text]
  24. Inferring protein-DNA dependencies using motif alignments and mutual information
    S Mahony, PE Auron, PV Benos
    Bioinformatics (2007) 23(13):i297-i304
    [Abstract] [Open Access Article]
  25. Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome
    S Mahony, DL Corcoran, E Feingold, PV Benos
    Genome Biology (2007) 8(5):R84
    [Abstract] [Open Access Article] [PMC Free Text]
  26. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequence
    TS Mikkelsen, MJ Wakefield, …, S Mahony (37 of 64), …, ES Lander, K Lindblad-Toh
    Nature (2007) 447:167-177
    [Abstract] [Article]
  27. STAMP: a web tool for exploring DNA-binding motif similarities
    S Mahony, PV Benos
    Nucleic Acids Research (2007) 35(Web Server issue):W253-W258
    [Abstract] [Open Access Article] [PMC Free Text]
  28. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies
    S Mahony, P Auron, PV Benos
    PLoS Computational Biology (2007) 3(3):e61
    [Abstract] [Open Access Article] [PMC Free Text]
  29. Gene prediction in metagenomic libraries using the self-organising map and high performance computing techniques
    N McCoy, S Mahony, A Golden
    Springer Lecture Notes in Bioinformatics (2007) 4360:99-110. (Proc. GCCB 2006)
    [Article]
  30. Self-organizing neural networks to support the discovery of DNA-binding motifs
    S Mahony, PV Benos, TJ Smith, A Golden
    Neural Networks (2006) 19(6-7):950-962
    [Abstract] [Article]
  31. Reconstructing an ancestral mammalian immune supercomplex from a marsupial MHC
    K Belov, JE Deakin, AT Papenfuss, ML Baker, HV Siddle, N Gouin, DL Goode, TJ Sargeant, MD Robinson, MJ Wakefield, S Mahony, JGR Cross, PV Benos, PB Samollow, TP Speed, JA Marshall Graves, RD Miller
    PLoS Biology (2006) 4(3):e46
    [Abstract] [Open Access Article] [PMC Free Text]
  32. Improved detection of DNA motifs using a self-organized clustering of familial binding profiles
    S Mahony, A Golden, TJ Smith, PV Benos
    Bioinformatics (2005) 21(Suppl 1):i283-i291 (Proc. ISMB 2005)
    [Abstract] [Free Article]
  33. Transcription factor binding site identification using the self-organizing map
    S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar
    Bioinformatics (2005) 21(9):1807-14
    [Abstract] [Free Article]
  34. Gene prediction using the self-organizing map: automatic generation of multiple gene models
    S Mahony, JO McInerney, TJ Smith, A Golden
    BMC Bioinformatics (2004) 5:23
    [Abstract] [Open Access Article] [PMC Free Text]