Publications

Unpublished Preprints

* co-first authors; † co-corresponding authors; group members in bold

3.	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 bioRxiv 2020.11.23.391771
2.	Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation S Pinglay, M Bulajić, DP Rahe, E Huang, R Brosh, S German, JA Cadley, L Rieber, N Easo, S Mahony, MT Maurano, LJ Holt, EO Mazzoni, JD Boeke bioRxiv 2021.07.07.451065
1.	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 bioRxiv 2021.07.26.453821

Journal Articles

* co-first authors; † co-corresponding authors; group members in bold

51.	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 Genome Research 2022 accepted
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 Nature 2021 592(7853):309-314
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 Bioinformatics 2021 37(18):3011-3
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 Genome Biology 2021 22(1):20
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 Molecular Microbiology 2021 10.1111/mmi.14676
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 Development 2020 147(22):dev.194761 [Cover Article]
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 Nucleic Acids Research 2020 gkaa618 [NAR Breakthrough Article]
44.	Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map T Kunz, L Rieber, S Mahony Methods 2020 S1046-2023(19)30277-4
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 Genome Research (2020) 30:472-484
42.	ChExMix: a method for identifying and classifying protein-DNA interaction subtypes N Yamada, PK Kuntala, BF Pugh, S Mahony Journal of Computational Biology (2020) 27(3):429-435
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 IUBMB Life (2020) 72(1):27-38 [review article]
40.	Direct prediction of regulatory elements from partial data without imputation Y Zhang, S Mahony PLoS Computational Biology (2019) 15(11):e1007399
39.	Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns D Srivastava, S Mahony BBA Gene Regulatory Mechanisms (2019) 19:194443 [review article]
38.	Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types L Rieber, S Mahony Epigenetics & Chromatin (2019) 12(1):61
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^† Nature Neuroscience (2019) 35(6):903-913
36.	Characterizing protein-DNA binding event subtypes in ChIP-exo data N Yamada, WKM Lai, N Farrell, BF Pugh, S Mahony Bioinformatics (2019) 35(6):903-913 [ISCB RegSys “top 10 reading papers of 2019”]
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 Genome Research (2018) 28:357-366
34.	Deconvolving sequence features that discriminate between overlapping regulatory annotations A Kakumanu, S Velasco, EO Mazzoni, S Mahony PLoS Computational Biology (2017) 13(10):e1005795
33.	miniMDS: 3D structural inference from high-resolution Hi-C data L Rieber, S Mahony Bioinformatics (2017) 33 (14):i261-i266
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^† Cell Stem Cell* (2017) 20(2):205-217.e8
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 Molecular Cell (2016) 62(1): 72-91
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 Cell Stem Cell (2016) 18(3):410-421
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 Pacific Symposium on Biocomputing (2016) 21:57-68
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 Molecular & Cell Biology (2016) 36(1):157-172
27.	Protein-DNA binding in high resolution S Mahony, BF Pugh Critical Reviews in Biochemistry and Molecular Biology (2015) 4:269-283 [review article]
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 Nature Neuroscience (2014) 17(8):1046-54
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^† *PLoS Computational Biology* (2014) 10(3):e1003501
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 Stem Cell Reports (2013) 1(5):425-436
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 Nature Neuroscience (2013) 16(9):1219-1227
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 Nature Neuroscience* (2013) 16(9):1191-1198
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 Nucleic Acids Research (2013) 41(2):e38
↓ 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^† PLoS Computational Biology (2012) 8(8):e1002638
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 Nature Methods (2011) 8(12):1056-1058
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 PLoS ONE (2011) 6(7):e22401
17.	Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis S Mahony, EO Mazzoni, S McCuine, RA Young, H Wichterle, DK Gifford Genome Biology (2011) 12(1):R2
16.	Discovering homotypic binding events at high spatial resolution Y Guo, G Papachristoudis, RC Altshuler, GK Gerber, TS Jaakkola, DK Gifford, S Mahony Bioinformatics (2010) 26(24):3028-3034
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 Neuron (2010) 67(5):781-796
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 Genetics (2010) 185:513-522
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 Nucleic Acids Research (2008) 36(Database issue):D107-13
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 Genome Biology (2007) 8(7):R146
11.	Inferring protein-DNA dependencies using motif alignments and mutual information S Mahony, PE Auron, PV Benos Bioinformatics (2007) 23(13):i297-i304
10.	Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome S Mahony, DL Corcoran, E Feingold, PV Benos Genome Biology (2007) 8(5):R84
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 Nature (2007) 447:167-177
8.	STAMP: a web tool for exploring DNA-binding motif similarities S Mahony, PV Benos Nucleic Acids Research (2007) 35(Web Server issue):W253-W258
7.	DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies S Mahony, P Auron, PV Benos PLoS Computational Biology (2007) 3(3):e61
6.	Gene prediction in metagenomic libraries using the self-organising map and high performance computing techniques N McCoy, S Mahony, A Golden Lecture Notes in Bioinformatics (2007) 4360:99-110. (Proc. GCCB 2006)
5.	Self-organizing neural networks to support the discovery of DNA-binding motifs S Mahony, PV Benos, TJ Smith, A Golden Neural Networks (2006) 19(6-7):950-962
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 PLoS Biology (2006) 4(3):e46
3.	Improved detection of DNA motifs using a self-organized clustering of familial binding profiles S Mahony, A Golden, TJ Smith, PV Benos Bioinformatics (2005) 21(Suppl 1):i283-i291 (Proc. ISMB 2005)
2.	Transcription factor binding site identification using the self-organizing map S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar Bioinformatics (2005) 21(9):1807-14
1.	Gene prediction using the self-organizing map: automatic generation of multiple gene models S Mahony, JO McInerney, TJ Smith, A Golden BMC Bioinformatics (2004) 5:23