Unpublished Preprints
* co-first authors; † co-corresponding authors; group members in bold
| 4. |
Perspective on recent developments and challenges in regulatory and systems genomics
J Zeitlinger, S Roy, F Ay, A Mathelier, A Medina-Rivera, S Mahony, S Sinha, J Ernst
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| 3. |
Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)
ST Bresnahan, S Mahony, K Anton, B Harpur, CM Grozinger
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| 2. |
Human CCR4-NOT globally regulates gene expression and is a novel silencer of retrotransposon activation
S Kulkarni, A Morrissey, A Sebastian, B Giardine, C Smith, OT Akinniyi, CA Keller, A Arnaoutov, I Albert, S Mahony, JC Reese
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| 1. |
Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin
S Arora*, J Yang*, T Akiyama, DQ James, A Morrissey, TR Blanda, N Badjatia, WKM Lai, MSH Ko, BF Pugh, S Mahony
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Journal Articles
* co-first authors; † co-corresponding authors; group members in bold
| 61. |
Systematic dissection of sequence features affecting the binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1
C Xu, H Kleinschmidt, J Yang, E Leith, J Johnson, S Tan, S Mahony, L Bai
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| 60. |
Sized-based expectation maximization for characterizing nucleosome positions and subtypes
J Yang, K Yen, S Mahony
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| 59. |
Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats
A Morrissey, J Shi, DQ James, S Mahony
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| 58. |
DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite, Plasmodium falciparum
V Bonnell, Y Zhang, A Brown, J Horton, G Josling, T-P Chiu, R Rohs, S Mahony, R Gordan, M Llinás
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| 57. |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
G Xiang, X He, BM Giardine, KJ Weaver, DJ Taylor, RC McCoy, C Jansen, CA Keller, AQ Wixom, A Cockburn, A Miller, Q Qi, Y He, Y Li, J Lichtenberg, EF Heuston, SM Anderson, J Luan, MW Vermunt, F Yue, MEG Sauria, MC Schatz, J Taylor, B Göttgens, JR Hughes, DR Higgs, MJ Weiss, Y Cheng, GA Blobel, D Bodine, Y Zhang, Q Li, S Mahony, RC Hardison
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| 56. |
The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles
JM Schreiber, CA Boix, JW Lee, H Li, Y Guan, C-C Chang, J-C Chang, A Hawkins-Hooker, B Schoelkopf, G Schweikert, M Rojas Carulla, A Canakoglu, F Guzzo, L Nanni, M Masseroli, MJ Carman, P Pinoli, C Hong, KY Yip, JP Spence, SS Batra, YS Song, S Mahony, Z Zhang, W Tan, Y Shen, Y Sun, M Shi, J Adrian, RS Sandstrom, N Farrell, JM Halow, K Lee, L Jiang, X Yang, CB Epstein, JS Strattan, MP Snyder, M Kellis, WS Noble, AB Kundaje
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| 55. |
Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation
S Pinglay, M Bulajić, DP Rahe, E Huang, R Brosh, NE Mamrak, BR King, S German, JA Cadley, L Rieber, N Easo, T Lionnet, S Mahony, MT Maurano, LJ Holt, EO Mazzoni, JD Boeke
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| 54. |
PEGR: a flexible management platform for reproducible epigenomic and genomic research
D Shao, GD Kellogg, A Nematbakhsh, P Kuntala, S Mahony, BF Pugh, WKM Lai
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| 53. |
Domain adaptive neural networks improve cross-species prediction of transcription factor binding
K Cochran, D Srivastava, A Shrikumar, A Balsubramani, RC Hardison, A Kundaje, S Mahony
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| 52. |
Foxa2 and Pet1 direct and indirect synergy drive serotonergic neuronal differentiation
B Aydin, M Sierk, M Moreno-Estelles, L Tejavibulya, N Kumar, N Flames†, S Mahony†, E Mazzoni†
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| 51. |
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes
G Garipler, C Lu, A Morrissey, LS Lopez-Zepeda, SE Vidal, B Aydin, M Stadtfeld, U Ohler, S Mahony, NE Sanjana, EO Mazzoni
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| 50. |
High resolution protein architecture of the budding yeast genome
MJ Rossi, PK Kuntala, WKM Lai, N Yamada, N Badjatia, C Mittal, G Kuzu, K Bocklund, NP Farrell, TR Blanda, JD Mairose, AV Basting, KS Mistretta, DJ Rocco, ES Perkinson, GD Kellogg, S Mahony, BF Pugh
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| 49 |
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types
G Xiang, BM Giardine, S Mahony, Y Zhang, RC Hardison
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| 48. |
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding
D Srivastava, B Aydin, EO Mazzoni, S Mahony
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| 47. |
The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation
S Singh, JM Santos, LM Orchard, N Yamada, R van Biljon, HJ Painter, S Mahony, M Llinas
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| 46. |
Hox binding specificity is directed by DNA sequence preferences and differential abilities to engage inaccessible chromatin
M Bulajić*, D Srivastava*, JS Dasen, H Wichterle, S Mahony, EO Mazzoni
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| 45. |
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes
N Yamada, MJ Rossi, N Farrell, BF Pugh, S Mahony
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| 44. |
Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map
T Kunz, L Rieber, S Mahony
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| 43. |
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
G Xiang, CA Keller, E Heuston, BM Giardine, L An, AQ Wixom, A Miller, A Cockburn, J Lichtenberg, B Göttgens, Q Li, D Bodine, S Mahony, J Taylor, GA Blobel, MJ Weiss, Y Cheng, F Yue, J Hughes, DR Higgs, Y Zhang, RC Hardison
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| 42. |
ChExMix: a method for identifying and classifying protein-DNA interaction subtypes
N Yamada, PK Kuntala, BF Pugh, S Mahony
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| 41. |
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells
RC Hardison, Y Zhang, CA Keller, G Xiang, EF Heuston, L An, J Lichtenberg, BM Giardine, D Bodine, S Mahony, Q Li, F Yue, MJ Weiss, GA Blobel, J Taylor, J Hughes, DR Higgs, B Göttgens
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| 40. |
Direct prediction of regulatory elements from partial data without imputation
Y Zhang, S Mahony
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| 39. |
Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns
D Srivastava, S Mahony
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| 38. |
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types
L Rieber, S Mahony
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| 37. |
Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes
B Aydin, A Kakumanu, M Rossillo, M Moreno-Estelles, G Garipler, N Ringstad, N Flames, S Mahony†, EO Mazzoni†
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| 36. |
Characterizing protein-DNA binding event subtypes in ChIP-exo data
N Yamada, WKM Lai, N Farrell, BF Pugh, S Mahony
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| 35. |
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock
V Vinayachandran, R Reja, MJ Rossi, B Park, L Rieber, C Mittal, S Mahony, BF Pugh
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| 34. |
Deconvolving sequence features that discriminate between overlapping regulatory annotations
A Kakumanu, S Velasco, EO Mazzoni, S Mahony
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| 33. |
miniMDS: 3D structural inference from high-resolution Hi-C data
L Rieber, S Mahony
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| 32. |
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†
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| 31. |
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
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| 30. |
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
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| 29. |
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
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| 28. |
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
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| 27. |
Protein-DNA binding in high resolution
S Mahony, BF Pugh
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| 26. |
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
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| 25. |
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†
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| 24. |
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
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| 23. |
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
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| 22. |
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
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| 21. |
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
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| ↓ BEFORE PENN STATE ↓ | |
| 20. |
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
Y Guo, S Mahony†, DK Gifford†
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| 19. |
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
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| 18. |
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
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| 17. |
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
S Mahony*, EO Mazzoni*, S McCuine, RA Young, H Wichterle, DK Gifford
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| 16. |
Discovering homotypic binding events at high spatial resolution
Y Guo, G Papachristoudis, RC Altshuler, GK Gerber, TS Jaakkola, DK Gifford, S Mahony
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| 15. |
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
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| 14. |
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
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| 13. |
ORegAnno: an open-access community-driven resource for regulatory annotation
OL Griffith, SB Montgomery, …, S Mahony (7 of 29 authors), …, CM Bergman, SJM Jones
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| 12. |
Combined analysis reveals a core set of cycling genes
Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden, Z Bar-Joseph
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| 11. |
Inferring protein-DNA dependencies using motif alignments and mutual information
S Mahony, PE Auron, PV Benos
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| 10. |
Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome
S Mahony, DL Corcoran, E Feingold, PV Benos
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| 9. |
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
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| 8. |
STAMP: a web tool for exploring DNA-binding motif similarities
S Mahony, PV Benos
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| 7. |
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies
S Mahony, P Auron, PV Benos
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| 6. |
Gene prediction in metagenomic libraries using the self-organising map and high performance computing techniques
N McCoy, S Mahony, A Golden
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| 5. |
Self-organizing neural networks to support the discovery of DNA-binding motifs
S Mahony, PV Benos, TJ Smith, A Golden
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| 4. |
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
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| 3. |
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles
S Mahony, A Golden, TJ Smith, PV Benos
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| 2. |
Transcription factor binding site identification using the self-organizing map
S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar
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| 1. |
Gene prediction using the self-organizing map: automatic generation of multiple gene models
S Mahony, JO McInerney, TJ Smith, A Golden
|