Shaun Mahony
Penn State University
H-index: 34
North America-United States
Top articles of Shaun Mahony
Title | Journal | Author(s) | Publication Date |
|---|---|---|---|
Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats | bioRxiv | Alexis Morrissey Jeffrey Shi Daniela Q James Shaun Mahony | 2023/9/15 |
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes | bioRxiv | Guanjue Xiang Xi He Belinda M Giardine Kathryn J Isaac Dylan J Taylor | 2023/11/21 |
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles | Genome biology | Jacob Schreiber Carles Boix Jin wook Lee Hongyang Li Yuanfang Guan | 2023/4/18 |
Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 | bioRxiv | Cheng Xu Holly Kleinschmidt Jianyu Yang Erik Leith Jenna Johnson | 2023/11/11 |
Dna Sequence Context and the Chromatin Landscape Differentiate Sequence-Specific Transcription Factor Binding in the Human Malaria Parasite Plasmodium Falciparum | Victoria Ann Bonnell | 2023 | |
SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes | bioRxiv | Jianyu Yang Kuangyu Yen Shaun Mahony | 2023/10/20 |
Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin | bioRxiv | Sonny Arora Jianyu Yang Tomohiko Akiyama Daniela Q James Alexis Morrissey | 2023/10/9 |
PEGR: a flexible management platform for reproducible epigenomic and genomic research | Genome biology | Danying Shao Gretta D Kellogg Ali Nematbakhsh Prashant K Kuntala Shaun Mahony | 2022/4/19 |
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes | Cell reports | Görkem Garipler Congyi Lu Alexis Morrissey Lorena S Lopez-Zepeda Yingzhen Pei | 2022/3/15 |
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding | Genome research | Kelly Cochran Divyanshi Srivastava Avanti Shrikumar Akshay Balsubramani Ross C Hardison | 2022/3/1 |
Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation | Science | Sudarshan Pinglay Milica Bulajić Dylan P Rahe Emily Huang Ran Brosh | 2022/7/1 |
Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation | Frontiers in Neuroscience | Begüm Aydin Michael Sierk Mireia Moreno-Estelles Link Tejavibulya Nikathan Kumar | 2022/6/20 |
The PfAP2‐G2 transcription factor is a critical regulator of gametocyte maturation | Molecular microbiology | Suprita Singh Joana M Santos Lindsey M Orchard Naomi Yamada Riëtte van Biljon | 2021/5 |
Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map | Methods | Timothy Kunz Lila Rieber Shaun Mahony | 2021/5/1 |
A high-resolution protein architecture of the budding yeast genome | Nature | Matthew J Rossi Prashant K Kuntala William KM Lai Naomi Yamada Nitika Badjatia | 2021/4/8 |
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding | Genome biology | Divyanshi Srivastava Begüm Aydin Esteban O Mazzoni Shaun Mahony | 2021/12 |
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types | Bioinformatics | Guanjue Xiang Belinda M Giardine Shaun Mahony Yu Zhang Ross C Hardison | 2021/9/15 |
PEGR: a management platform for ChIP-based next generation sequencing pipelines | Danying Shao Gretta Kellogg Shaun Mahony William Lai B Franklin Pugh | 2020/7/26 | |
Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns | Divyanshi Srivastava Shaun Mahony | 2020/6/1 | |
ChExMix: a method for identifying and classifying protein–DNA interaction subtypes | Journal of Computational Biology | Naomi Yamada Prashant Kumar Kuntala B Franklin Pugh Shaun Mahony | 2020/3/1 |
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