S
Shaun Mahony
Researcher at Pennsylvania State University
Publications - 92
Citations - 5172
Shaun Mahony is an academic researcher from Pennsylvania State University. The author has contributed to research in topics: Transcription factor & Chromatin. The author has an hindex of 32, co-authored 85 publications receiving 4397 citations. Previous affiliations of Shaun Mahony include Brigham and Women's Hospital & University of Pittsburgh.
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Journal ArticleDOI
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Matthew Wakefield,Bronwen Aken,Chris T. Amemiya,Jean L. Chang,Shannon E. Duke,Manuel Garber,Andrew J. Gentles,Andrew J. Gentles,Leo Goodstadt,Andreas Heger,Jerzy Jurka,Michael Kamal,Evan Mauceli,Stephen M. J. Searle,Ted Sharpe,Michelle L. Baker,Mark A. Batzer,Panayiotis V. Benos,Katherine Belov,Michele Clamp,April Cook,James Cuff,Radhika Das,Lance S. Davidow,Janine E. Deakin,Melissa Fazzari,Jacob L. Glass,Manfred Grabherr,John M. Greally,Wanjun Gu,Timothy A. Hore,Gavin A. Huttley,Michael Kleber,Randy L. Jirtle,Edda Koina,Jeannie T. Lee,Shaun Mahony,Marco A. Marra,Robert D. Miller,Robert D. Nicholls,Mayumi Oda,Anthony T. Papenfuss,Zuly E. Parra,David D. Pollock,David A. Ray,Jacqueline E. Schein,Terence P. Speed,Katherine Thompson,John L. VandeBerg,Claire M. Wade,Claire M. Wade,Jerilyn A. Walker,Paul D. Waters,Caleb Webber,Jennifer R. Weidman,Xiaohui Xie,Michael C. Zody,Jennifer Baldwin,Amr Abdouelleil,Jamal Abdulkadir,Adal Abebe,Brikti Abera,Justin Abreu,St Christophe Acer,Lynne Aftuck,Allen Alexander,Peter An,Erica Anderson,Scott Anderson,Harindra Arachi,Marc Azer,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Aaron M. Berlin,Daniel Bessette,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Imane Bourzgui,Adam Brown,Patrick Cahill,Sheridon Channer,Yama Cheshatsang,Lisa Chuda,Mieke Citroen,Alville Collymore,Patrick Cooke,Maura Costello,Katie D'Aco,Riza M. Daza,Georgius De Haan,Stuart DeGray,Christina Demaso,Norbu Dhargay,Kimberly Dooley,Erin E. Dooley,Missole Doricent,Passang Dorje,Kunsang Dorjee,Alan Dupes,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Sheila Fisher,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Loryn Gadbois,Gary Gearin,Christina R. Gearin,Georgia Giannoukos,Tina Goode,Joseph Graham,Edward Grandbois,Sharleen Grewal,Kunsang Gyaltsen,Nabil Hafez,Birhane Hagos,Jennifer L. Hall,Charlotte Henson,Andrew Hollinger,Tracey Honan,Monika D. Huard,Leanne Hughes,Brian Hurhula,M. Erii Husby,Asha Kamat,Ben Kanga,Seva Kashin,Dmitry Khazanovich,Peter Kisner,Krista Lance,Marcia Lara,William Lee,Niall J. Lennon,Frances Letendre,Rosie Levine,Alex Lipovsky,Xiaohong Liu,Jinlei Liu,Shangtao Liu,Tashi Lokyitsang,Yeshi Lokyitsang,Rakela Lubonja,Annie Lui,Pen MacDonald,Vasilia Magnisalis,Kebede Maru,Charles Matthews,William McCusker,Susan McDonough,Teena Mehta,James Meldrim,Louis Meneus,Oana Mihai,Atanas Mihalev,Tanya Mihova,Rachel Mittelman,Valentine Mlenga,Anna Montmayeur,Leonidas Mulrain,Adam Navidi,Jerome Naylor,Tamrat Negash,Thu Nguyen,Nga Nguyen,Robert Nicol,Choe Norbu,Nyima Norbu,Nathaniel Novod,Barry O'Neill,Sahal Osman,Eva Markiewicz,Otero L. Oyono,Christopher Patti,Pema Phunkhang,Fritz Pierre,Margaret Priest,Sujaa Raghuraman,Filip Rege,Rebecca Reyes,Cecil Rise,Peter Rogov,Keenan Ross,Elizabeth P. Ryan,Sampath Settipalli,Terry Shea,Ngawang Sherpa,Lu Shi,Diana Shih,Todd Sparrow,Jessica Spaulding,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Christopher Strader,Senait Tesfaye,Talene Thomson,Yama Thoulutsang,Dawa Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane Wilkinson,Adam Wilson,Shailendra Yadav,Geneva Young,Qing Yu,Lisa Zembek,Danni Zhong,Andrew Zimmer,Zac Zwirko,David B. Jaffe,Pablo Alvarez,William Brockman,Jonathan Butler,Chee Whye Chin,Sante Gnerre,Iain MacCallum,Jennifer A. Marshall Graves,Chris P. Ponting,Matthew Breen,Paul B. Samollow,Eric S. Lander,Eric S. Lander,Kerstin Lindblad-Toh +238 more
TL;DR: A high-quality draft of the genome sequence of the grey, short-tailed opossum is reported, indicating a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation.
Journal ArticleDOI
STAMP: a web tool for exploring DNA-binding motif similarities
Shaun Mahony,Panayiotis V. Benos +1 more
TL;DR: STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs, and is a highly flexible alignment platform, allowing users to ‘mix-and-match’ between various implemented comparison metrics, alignment methods, multiple alignment strategies and tree-building methods.
Journal ArticleDOI
The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.
Makiko Iwafuchi-Doi,Greg Donahue,Akshay Kakumanu,Jason A. Watts,Shaun Mahony,B. Franklin Pugh,Dolim Lee,Klaus H. Kaestner,Kenneth S. Zaret +8 more
TL;DR: It is found that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers, suggesting nucleosome are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.
Journal ArticleDOI
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
TL;DR: In this paper, a new integrative computational method, genome wide event finding and motif discovery (GEM), was developed to discover novel transcription factor spatial binding constraints in vivo. But the method is not suitable for the analysis of large-scale data sets.
Journal ArticleDOI
ORegAnno: an open-access community-driven resource for regulatory annotation.
Obi L. Griffith,Stephen B. Montgomery,Bridget Bernier,Bryan Chu,Katayoon Kasaian,Stein Aerts,Shaun Mahony,Monica C. Sleumer,Mikhail Bilenky,Maximilian Haeussler,Malachi Griffith,Steven M. Gallo,Belinda Giardine,Bart Hooghe,Peter Van Loo,Enrique Blanco,Amy Ticoll,Stuart Lithwick,Elodie Portales-Casamar,Ian J. Donaldson,Gordon Robertson,Claes Wadelius,Pieter De Bleser,D. Vlieghe,Marc S. Halfon,Wyeth W. Wasserman,Ross C. Hardison,Casey M. Bergman,Steven J.M. Jones +28 more
TL;DR: The current release of ORegAnno comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species.