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1

Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene

Heekyung Jung, Julie Lacombe, Esteban O. Mazzoni, Karel F. Liem Jr., Jonathan Grinstein, Shaun Mahony, Debnath Mukhopadhyay, David K. Gifford, Richard A. Young, Kathryn V. Anderson, Hynek Wichterle, J

Journal:

Year:

2010

Language:

english

File:

PDF, 3.98 MB

english, 2010

2

Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences

Shaun Mahony, David Hendrix, Terry J. Smith, Aaron Golden

Journal:

Artificial Intelligence Review

Year:

2005

Language:

english

File:

PDF, 184 KB

english, 2005

3

Constructing and deconstructing spinal motor neurons

Mazzoni, Esteban O., Mahony, Shaun, Morrison, Carolyn A., Nedelec, Stephane, Gifford, David K., Wichterle, Hynek

Journal:

International Journal of Developmental Neuroscience

Year:

2012

Language:

english

File:

PDF, 46 KB

english, 2012

4

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

Shaun Mahony, David L Corcoran, Eleanor Feingold, Panayiotis V Benos

Journal:

Year:

2007

Language:

english

File:

PDF, 560 KB

english, 2007

5

Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque

Zinman, Guy, Brower-Sinning, Rachel, Emeche, Chineye H., Ernst, Jason, Huang, Grace Tzu-Wei, Mahony, Shaun, Myers, Amy J., O'Dee, Dawn M., Flynn, JoAnne L., Nau, Gerard J., Ross, Ted M., Salter, Russe

Journal:

Year:

2011

Language:

english

File:

PDF, 674 KB

english, 2011

6

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models

Shaun Mahony, James O McInerney, Terry J Smith, Aaron Golden

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 432 KB

english, 2004

7

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

Aydin, Begüm, Kakumanu, Akshay, Rossillo, Mary, Moreno-Estellés, Mireia, Garipler, Görkem, Ringstad, Niels, Flames, Nuria, Mahony, Shaun, Mazzoni, Esteban O.

Journal:

Nature Neuroscience

Year:

2019

Language:

english

File:

PDF, 4.17 MB

english, 2019

8

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

Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden

Journal:

Neural Networks

Year:

2006

Language:

english

File:

PDF, 1.07 MB

english, 2006

9

ChExMix: A Method for Identifying and Classifying ProteinâDNA Interaction Subtypes

Yamada, Naomi, Kuntala, Prashant Kumar, Pugh, B. Franklin, Mahony, Shaun

Journal:

Journal of Computational Biology

Year:

2020

File:

PDF, 487 KB

2020

10

Modulation of pathogen-induced CCL20 secretion from HT-29 human intestinal epithelial cells by commensal bacteria

Shomik Sibartie, Ann M O'Hara, Jude Ryan, Áine Fanning, Jim O'Mahony, Shaun O'Neill, Barbara Sheil, Liam O'Mahony, Fergus Shanahan

Journal:

Year:

2009

Language:

english

File:

PDF, 520 KB

english, 2009

11

Differential abilities to engage inaccessible chromatin diversify vertebrate HOX binding patterns

BulajiÄ, Milica, Srivastava, Divyanshi, Dasen, Jeremy S., Wichterle, Hynek, Mahony, Shaun, Mazzoni, Esteban O.

Journal:

Development (The Company of Biologists)

Year:

2020

File:

PDF, 7.20 MB

2020

12

Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map

Kunz, Timothy, Rieber, Lila, Mahony, Shaun

Journal:

Year:

2020

File:

PDF, 2.91 MB

2020

13

Protein–DNA binding in high-resolution

Mahony, Shaun, Pugh, B. Franklin

Journal:

Critical Reviews in Biochemistry and Molecular Biology

Year:

2015

Language:

english

File:

PDF, 715 KB

english, 2015

14

[ACM Press CHI '03 extended abstracts - Ft. Lauderdale, Florida, USA (2003.04.05-2003.04.10)] CHI '03 extended abstracts on Human factors in computing systems - CHI '03 - PENPETS

O'Mahony, Shaun, Robinson, John A.

Year:

2003

Language:

english

File:

PDF, 224 KB

english, 2003

15

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (4 – 8 January 2016)] Biocomputing 2016 - PHENOME-WIDE INTERACTION STUDY (PheWIS) IN AIDS CLINICAL TRIALS GROUP DATA (ACTG)

VERMA, SHEFALI S., FRASE, ALEX T., VERMA, ANURAG, PENDERGRASS, SARAH A., MAHONY, SHAUN, HAAS, DAVID W., RITCHIE, MARYLYN D.

Language:

english

File:

PDF, 2.20 MB

english

16

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

Rieber, Lila, Mahony, Shaun

Journal:

Year:

2017

Language:

english

File:

PDF, 694 KB

english, 2017

17

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

Mazzoni, Esteban O, Mahony, Shaun, Closser, Michael, Morrison, Carolyn A, Nedelec, Stephane, Williams, Damian J, An, Disi, Gifford, David K, Wichterle, Hynek

Journal:

Nature Neuroscience

Year:

2013

Language:

english

File:

PDF, 1.82 MB

english, 2013

18

A Cdx4-Sall4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic Hematopoiesis

Paik, Elizabeth J., Mahony, Shaun, White, Richard M., Price, Emily N., DiBiase, Anthony, Dorjsuren, Bilguujin, Mosimann, Christian, Davidson, Alan J., Gifford, David, Zon, Leonard I.

Journal:

Stem Cell Reports

Year:

2013

Language:

english

File:

PDF, 2.30 MB

english, 2013

19

Combined analysis reveals a core set of cycling genes

Yong Lu, Shaun Mahony, Panayiotis V Benos, Roni Rosenfeld, Itamar Simon…

Journal:

Year:

2007

Language:

english

File:

PDF, 454 KB

english, 2007

20

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies

Mahony, Shaun, Auron, Philip E., Benos, Panayiotis V.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.05 MB

english, 2007

21

Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of proteinâDNA complexes

Yamada, Naomi, Rossi, Matthew J, Farrell, Nina, Pugh, B Franklin, Mahony, Shaun

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 4.05 MB

2020

22

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

Iwafuchi-Doi, Makiko, Donahue, Greg, Kakumanu, Akshay, Watts, Jason A., Mahony, Shaun, Pugh, B. Franklin, Lee, Dolim, Kaestner, Klaus H., Zaret, Kenneth S.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.16 MB

english, 2016

23

Real-world comparative analysis of bleeding complications and health-related quality of life in patients with haemophilia A and haemophilia B

Booth, Jason, Oladapo, Abiola, Walsh, Shaun, O'Hara, Jamie, Carroll, Liz, Garcia Diego, Daniel-Anibal, O'Mahony, Brian

Journal:

Year:

2018

Language:

english

File:

PDF, 420 KB

english, 2018

24

Genome-wide organization of GATA1 and TAL1 determined at high resolution

Han, G. Celine, Vinayachandran, Vinesh, Bataille, Alain R., Park, Bongsoo, Chan-Salis, Ka Yim, Keller, Cheryl A., Long, Maria, Mahony, Shaun, Hardison, Ross C., Pugh, B. Franklin

Journal:

Molecular and Cellular Biology

Year:

2015

Language:

english

File:

PDF, 9.41 MB

english, 2015

25

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

Shaun Mahony, Esteban O Mazzoni, Scott McCuine, Richard A Young…

Journal:

Year:

2011

Language:

english

File:

PDF, 1.33 MB

english, 2011

26

Embryonic stem cell–based mapping of developmental transcriptional programs

Mazzoni, Esteban O, Mahony, Shaun, Iacovino, Michelina, Morrison, Carolyn A, Mountoufaris, George, Closser, Michael, Whyte, Warren A, Young, Richard A, Kyba, Michael, Gifford, David K, Wichterle, Hyne

Journal:

Year:

2011

Language:

english

File:

PDF, 670 KB

english, 2011

27

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

Hardison, Ross C., Zhang, Yu, Keller, Cheryl A., Xiang, Guanjue, Heuston, Elisabeth F., An, Lin, Lichtenberg, Jens, Giardine, Belinda M., Bodine, David, Mahony, Shaun, Li, Qunhua, Yue, Feng, Weiss, Mi

Journal:

Year:

2019

File:

PDF, 1.96 MB

2019

28

Mycobacterium avium subsp. Paratuberculosis (MAP) as a modifying factor in Crohn's disease

Shomik Sibartie, Paul Scully, John Keohane, Shaun O'Neill, Jim O'Mahony, Deirdre O'Hanlon, William O. Kirwan, Liam O'Mahony, Fergus Shanahan

Journal:

Inflammatory Bowel Diseases

Year:

2010

Language:

english

File:

PDF, 471 KB

english, 2010

29

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

Yamada, Naomi, Lai, William K M, Farrell, Nina, Pugh, B Franklin, Mahony, Shaun, Birol, Inanc

Journal:

Year:

2018

Language:

english

File:

PDF, 1.04 MB

english, 2018

30

Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types

Rieber, Lila, Mahony, Shaun

Journal:

Epigenetics & Chromatin

Year:

2019

Language:

english

File:

PDF, 4.25 MB

english, 2019

31

Direct prediction of regulatory elements from partial data without imputation

Zhang, Yu, Mahony, Shaun, Roy, Sushmita

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 6.64 MB

english, 2019

32

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

Vinayachandran, Vinesh, Reja, Rohit, Rossi, Matthew J., Park, Bongsoo, Rieber, Lila, Mittal, Chitvan, Mahony, Shaun, Pugh, B. Franklin

Journal:

Genome Research

Year:

2018

Language:

english

File:

PDF, 2.09 MB

english, 2018

33

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

Lodato, Simona, Molyneaux, Bradley J, Zuccaro, Emanuela, Goff, Loyal A, Chen, Hsu-Hsin, Yuan, Wen, Meleski, Alyssa, Takahashi, Emi, Mahony, Shaun, Rinn, John L, Gifford, David K, Arlotta, Paola

Journal:

Nature Neuroscience

Year:

2014

Language:

english

File:

PDF, 2.33 MB

english, 2014

34

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

Velasco, Silvia, Ibrahim, Mahmoud M., Kakumanu, Akshay, Garipler, Görkem, Aydin, Begüm, Al-Sayegh, Mohamed Ahmed, Hirsekorn, Antje, Abdul-Rahman, Farah, Satija, Rahul, Ohler, Uwe, Mahony, Shaun, Mazzo

Journal:

Year:

2017

Language:

english

File:

PDF, 4.49 MB

english, 2017

35

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

Mazzoni, Esteban O, Mahony, Shaun, Peljto, Mirza, Patel, Tulsi, Thornton, Seraphim R, McCuine, Scott, Reeder, Christopher, Boyer, Laurie A, Young, Richard A, Gifford, David K, Wichterle, Hynek

Journal:

Nature Neuroscience

Year:

2013

Language:

english

File:

PDF, 1.73 MB

english, 2013

36

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Mahony, Shaun, Edwards, Matthew D., Mazzoni, Esteban O., Sherwood, Richard I., Kakumanu, Akshay, Morrison, Carolyn A., Wichterle, Hynek, Gifford, David K., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.17 MB

english, 2014

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