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Items: 12

1.

High-throughput functional comparison of promoter and enhancer activities.

Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, Gray JM.

Genome Res. 2016 Aug;26(8):1023-33. doi: 10.1101/gr.204834.116. Epub 2016 Jun 16.

2.

The transcription factor calcium-response factor limits NMDA receptor-dependent transcription in the developing brain.

Lyons MR, Chen LF, Deng JV, Finn C, Pfenning AR, Sabhlok A, Wilson KM, West AE.

J Neurochem. 2016 Apr;137(2):164-76. doi: 10.1111/jnc.13556. Epub 2016 Feb 15.

3.

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes.

Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH.

Cell. 2015 Jun 18;161(7):1592-605. doi: 10.1016/j.cell.2015.05.032. Epub 2015 Jun 4.

4.

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease.

Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M.

Nature. 2015 Feb 19;518(7539):365-9. doi: 10.1038/nature14252.

5.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

6.

Convergent transcriptional specializations in the brains of humans and song-learning birds.

Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256846. doi: 10.1126/science.1256846.

7.

Core and region-enriched networks of behaviorally regulated genes and the singing genome.

Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256780. doi: 10.1126/science.1256780.

8.

Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities.

Chen CC, Winkler CM, Pfenning AR, Jarvis ED.

J Comp Neurol. 2013 Nov;521(16):3666-701. doi: 10.1002/cne.23406.

9.

Relation of addiction genes to hypothalamic gene changes subserving genesis and gratification of a classic instinct, sodium appetite.

Liedtke WB, McKinley MJ, Walker LL, Zhang H, Pfenning AR, Drago J, Hochendoner SJ, Hilton DL, Lawrence AJ, Denton DA.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12509-14. doi: 10.1073/pnas.1109199108. Epub 2011 Jul 11.

10.

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways.

Pfenning AR, Kim TK, Spotts JM, Hemberg M, Su D, West AE.

PLoS One. 2010 May 27;5(5):e10870. doi: 10.1371/journal.pone.0010870.

11.

The genome of a songbird.

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.

Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819.

12.

A comparative genomics approach to identifying the plasticity transcriptome.

Pfenning AR, Schwartz R, Barth AL.

BMC Neurosci. 2007 Mar 13;8:20.

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