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Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.

Aydin B, Kakumanu A, Rossillo M, Moreno-Estellés M, Garipler G, Ringstad N, Flames N, Mahony S, Mazzoni EO.

Nat Neurosci. 2019 Jun;22(6):897-908. doi: 10.1038/s41593-019-0399-y. Epub 2019 May 13.


Six new Cyrtodactylus (Squamata: Gekkonidae) from northeast India.

Agarwal I, Mahony S, Giri VB, Chaitanya R, Bauer AM.

Zootaxa. 2018 Nov 25;4524(5):501-535. doi: 10.11646/zootaxa.4524.5.1.


Two new and potentially highly threatened Megophrys Horned frogs (Amphibia: Megophryidae) from Indochina's highest mountains.

Tapley B, Cutajar T, Mahony S, Nguyen CT, Dau VQ, Luong AM, Le DT, Nguyen TT, Nguyen TQ, Portway C, Luong HV, Rowley JJL.

Zootaxa. 2018 Oct 31;4508(3):301-333. doi: 10.11646/zootaxa.4508.3.1.


Two new species of bent toed geckos, Cyrtodactylus Gray, 1827 (Squamata: Gekkonidae) from Northeast India with comments on name-bearing types from the region.

Agarwal I, Mahony S, Giri VB, Chaitanya R, Bauer AM.

Zootaxa. 2018 May 17;4420(3):334-356. doi: 10.11646/zootaxa.4420.3.2.


Characterizing protein-DNA binding event subtypes in ChIP-exo data.

Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S.

Bioinformatics. 2019 Mar 15;35(6):903-913. doi: 10.1093/bioinformatics/bty703.


Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock.

Vinayachandran V, Reja R, Rossi MJ, Park B, Rieber L, Mittal C, Mahony S, Pugh BF.

Genome Res. 2018 Feb 14. doi: 10.1101/gr.226761.117. [Epub ahead of print]


The Vietnamese population of <i>Megophrys</i> <i>kuatunensis</i> (Amphibia: Megophryidae) represents a new species of Asian horned frog from Vietnam and southern China.

Tapley B, Cutajar T, Mahony S, Nguyen CT, Dau VQ, Nguyen TT, Luong HV, Rowley JJL.

Zootaxa. 2017 Nov 8;4344(3):465-492. doi: 10.11646/zootaxa.4344.3.3.


Deconvolving sequence features that discriminate between overlapping regulatory annotations.

Kakumanu A, Velasco S, Mazzoni E, Mahony S.

PLoS Comput Biol. 2017 Oct 19;13(10):e1005795. doi: 10.1371/journal.pcbi.1005795. eCollection 2017 Oct.


miniMDS: 3D structural inference from high-resolution Hi-C data.

Rieber L, Mahony S.

Bioinformatics. 2017 Jul 15;33(14):i261-i266. doi: 10.1093/bioinformatics/btx271.


Molecular, morphological and acoustic assessment of the genus Ophryophryne (Anura, Megophryidae) from Langbian Plateau, southern Vietnam, with description of a new species.

Poyarkov NA Jr, Duong TV, Orlov NL, Gogoleva SS, Vassilieva AB, Nguyen LT, Nguyen VDH, Nguyen SN, Che J, Mahony S.

Zookeys. 2017 May 3;(672):49-120. doi: 10.3897/zookeys.672.10624. eCollection 2017.


Evolutionary History of the Asian Horned Frogs (Megophryinae): Integrative Approaches to Timetree Dating in the Absence of a Fossil Record.

Mahony S, Foley NM, Biju SD, Teeling EC.

Mol Biol Evol. 2017 Mar 1;34(3):744-771. doi: 10.1093/molbev/msw267.


A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells.

Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO.

Cell Stem Cell. 2017 Feb 2;20(2):205-217.e8. doi: 10.1016/j.stem.2016.11.006. Epub 2016 Dec 8.


Increased rates of large-magnitude explosive eruptions in Japan in the late Neogene and Quaternary.

Mahony SH, Sparks RS, Wallace LM, Engwell SL, Scourse EM, Barnard NH, Kandlbauer J, Brown SK.

Geochem Geophys Geosyst. 2016 Jul;17(7):2467-2479. Epub 2016 Jul 1.


An Irish outbreak of New Delhi metallo-β-lactamase (NDM)-1 carbapenemase-producing Enterobacteriaceae: increasing but unrecognized prevalence.

O'Connor C, Cormican M, Boo TW, McGrath E, Slevin B, O'Gorman A, Commane M, Mahony S, O'Donovan E, Powell J, Monahan R, Finnegan C, Kiernan MG, Coffey JC, Power L, O'Connell NH, Dunne CP.

J Hosp Infect. 2016 Dec;94(4):351-357. doi: 10.1016/j.jhin.2016.08.005. Epub 2016 Aug 19.


Improving nurses' access to healthcare evidence.

Anton L, Morris N, Mahony SI.

Nurs Times. 2016 Mar 9-15;112(10):17-9.


The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.

Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS.

Mol Cell. 2016 Apr 7;62(1):79-91. doi: 10.1016/j.molcel.2016.03.001.


Reprogrammed Stomach Tissue as a Renewable Source of Functional β Cells for Blood Glucose Regulation.

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.

Cell Stem Cell. 2016 Mar 3;18(3):410-21. doi: 10.1016/j.stem.2016.01.003. Epub 2016 Feb 18.


Frankixalus, a New Rhacophorid Genus of Tree Hole Breeding Frogs with Oophagous Tadpoles.

Biju SD, Senevirathne G, Garg S, Mahony S, Kamei RG, Thomas A, Shouche Y, Raxworthy CJ, Meegaskumbura M, Van Bocxlaer I.

PLoS One. 2016 Jan 20;11(1):e0145727. doi: 10.1371/journal.pone.0145727. eCollection 2016.



Verma SS, Frase AT, Verma A, Pendergrass SA, Mahony S, Haas DW, Ritchie MD.

Pac Symp Biocomput. 2016;21:57-68.


Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution.

Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, Long M, Mahony S, Hardison RC, Pugh BF.

Mol Cell Biol. 2015 Oct 26;36(1):157-72. doi: 10.1128/MCB.00806-15. Print 2016 Jan 1.


Protein-DNA binding in high-resolution.

Mahony S, Pugh BF.

Crit Rev Biochem Mol Biol. 2015;50(4):269-83. doi: 10.3109/10409238.2015.1051505. Epub 2015 Jun 3. Review.


Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons.

Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P.

Nat Neurosci. 2014 Aug;17(8):1046-54. doi: 10.1038/nn.3757. Epub 2014 Jul 6.


An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding.

Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003501. doi: 10.1371/journal.pcbi.1003501. eCollection 2014 Mar.


A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis.

Paik EJ, Mahony S, White RM, Price EN, Dibiase A, Dorjsuren B, Mosimann C, Davidson AJ, Gifford D, Zon LI.

Stem Cell Reports. 2013 Nov 7;1(5):425-36. doi: 10.1016/j.stemcr.2013.10.001. eCollection 2013.


Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.

Mazzoni EO, Mahony S, Peljto M, Patel T, Thornton SR, McCuine S, Reeder C, Boyer LA, Young RA, Gifford DK, Wichterle H.

Nat Neurosci. 2013 Sep;16(9):1191-1198. doi: 10.1038/nn.3490. Epub 2013 Aug 18.


Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity.

Mazzoni EO, Mahony S, Closser M, Morrison CA, Nedelec S, Williams DJ, An D, Gifford DK, Wichterle H.

Nat Neurosci. 2013 Sep;16(9):1219-27. doi: 10.1038/nn.3467. Epub 2013 Jul 21.


A multi-parametric flow cytometric assay to analyze DNA-protein interactions.

Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI.

Nucleic Acids Res. 2013 Jan;41(2):e38. doi: 10.1093/nar/gks1034. Epub 2012 Nov 11.


High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

Guo Y, Mahony S, Gifford DK.

PLoS Comput Biol. 2012;8(8):e1002638. doi: 10.1371/journal.pcbi.1002638. Epub 2012 Aug 9.


Embryonic stem cell-based mapping of developmental transcriptional programs.

Mazzoni EO, Mahony S, Iacovino M, Morrison CA, Mountoufaris G, Closser M, Whyte WA, Young RA, Kyba M, Gifford DK, Wichterle H.

Nat Methods. 2011 Nov 13;8(12):1056-8. doi: 10.1038/nmeth.1775.


Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque.

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.

PLoS One. 2011;6(7):e22401. doi: 10.1371/journal.pone.0022401. Epub 2011 Jul 18.


Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis.

Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK.

Genome Biol. 2011;12(1):R2. doi: 10.1186/gb-2011-12-1-r2. Epub 2011 Jan 13.


Discovering homotypic binding events at high spatial resolution.

Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S.

Bioinformatics. 2010 Dec 15;26(24):3028-34. doi: 10.1093/bioinformatics/btq590. Epub 2010 Oct 21.


Global control of motor neuron topography mediated by the repressive actions of a single hox gene.

Jung H, Lacombe J, Mazzoni EO, Liem KF Jr, Grinstein J, Mahony S, Mukhopadhyay D, Gifford DK, Young RA, Anderson KV, Wichterle H, Dasen JS.

Neuron. 2010 Sep 9;67(5):781-96. doi: 10.1016/j.neuron.2010.08.008.


Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast.

Wolf JJ, Dowell RD, Mahony S, Rabani M, Gifford DK, Fink GR.

Genetics. 2010 Jun;185(2):513-22. doi: 10.1534/genetics.110.113944. Epub 2010 Apr 9.


Preliminary report of a palliative care and case management project in an emergency department for chronically ill elderly patients.

Mahony SO, Blank A, Simpson J, Persaud J, Huvane B, McAllen S, Davitt M, McHugh M, Hutcheson A, Karakas S, Higgins P, Selwyn P.

J Urban Health. 2008 May;85(3):443-51. doi: 10.1007/s11524-008-9257-z.


ORegAnno: an open-access community-driven resource for regulatory annotation.

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; Open Regulatory Annotation Consortium.

Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. Epub 2007 Nov 15.


Combined analysis reveals a core set of cycling genes.

Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z.

Genome Biol. 2007;8(7):R146.


Inferring protein-DNA dependencies using motif alignments and mutual information.

Mahony S, Auron PE, Benos PV.

Bioinformatics. 2007 Jul 1;23(13):i297-304.


Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

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; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K.

Nature. 2007 May 10;447(7141):167-77.


STAMP: a web tool for exploring DNA-binding motif similarities.

Mahony S, Benos PV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W253-8. Epub 2007 May 3.


DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

Mahony S, Auron PE, Benos PV.

PLoS Comput Biol. 2007 Mar 30;3(3):e61. Epub 2007 Feb 15.


Self-organizing neural networks to support the discovery of DNA-binding motifs.

Mahony S, Benos PV, Smith TJ, Golden A.

Neural Netw. 2006 Jul-Aug;19(6-7):950-62. Epub 2006 Jul 12.


Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.

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.

PLoS Biol. 2006 Mar;4(3):e46. Epub 2006 Jan 31.


Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.

Mahony S, Golden A, Smith TJ, Benos PV.

Bioinformatics. 2005 Jun;21 Suppl 1:i283-91.


Transcription factor binding site identification using the self-organizing map.

Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS.

Bioinformatics. 2005 May 1;21(9):1807-14. Epub 2005 Jan 12.


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