Publications

2024

• Phan BN, Ray MH, Xue X, Fu C, Fenster RJ, Kohut SJ, Bergman J, Haber SN, McCullough KM, Fish MK, Glausier JR, Su Q, Tipton AE, Lewis DA, Freyberg Z, Tseng GC, Russek SJ, Alekseyev Y, Ressler KJ, Seney ML, Pfenning AR, Logan RW. Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder. (2024) Nat Commun. PMID: 38296993.
• Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E; Zoonomia Consortium; Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. (2024) Science. PMID: 38422184.
• Arokiaraj CM, Leone MJ, Kleyman M, Chamessian A, Phan BN, Bettega C. Lopes, Cherupally V, Noh MC, Corrigan KA, Yeramosu D, Franusich ME, Podder R, Lele S, Shiers S, Kang B, Kennedy MM, Chen V, Chen Z, Dum RP, Lewis DA, Qadri Y, Price TJ, Pfenning AR, Seal RP. 2023. Spatial, transcriptomic and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition. bioRxiv doi: 10.1101/2022.04.01.486135v2

2023

• Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP; Zoonomia Consortium; Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. (2023) Science. PMID: 37104615.
• Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. (2023) Science. PMID: 37104599.
• Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J; Zoonomia Consortium; Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. (2023) Science. PMID: 37104612.
• Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O’Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. (2023) Cell. PMID: 36638792
• Redich RW, Kowalczyk A, Tene M, Sestili HH, Foley K, Saputra E, Clark N, Chikina M, Meyer WK, Pfenning AR. 2023. RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution. bioRxiv doi: 10.1101/2023.12.06.570425v1

2022

• Welch GM, Boix CA, Schmauch E, Davila-Velderrain J, Victor MB, Dileep V, Bozzelli PL, Su Q, Cheng JD, Lee A, Leary NS, Pfenning AR, Kellis M, Tsai LH. Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration. (2022) Sci Adv. PMID: 36170369
• Lawler AJ, Ramamurthy E, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin M, Zhang X, Phan BN, Fox GA, Wade K, He J, Ozturk BE, Byrne LC, Stauffer WR, Fish KN, Pfenning AR. Machine learning sequence prioritization for cell type-specific enhancer design. (2022) Elife. PMID: 35576146
• Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AR, Kleyman M, Pfenning AR. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin. (2022) BMC Genomics. PMID: 35410163
• Xue X, Zong W, Glausier JR, Kim SM, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Seney ML, Logan RW. Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder. (2022) Transl Psychiatry. PMID: 35347109
• Clugston A, Bodnar A, Cerqueira DM, Phua YL, Lawler A, Boggs K, Pfenning AR, Ho J, Kostka D. Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development. (2022) Genomics. PMID: 34942352
• Brown AR, Fox GA, Kaplow IM, Lawler AJ, Phan BN, Wirthlin ME, Ramamurthy E, May GE, Chen Z, Su Q, McManus CJ, Pfenning AR. 2022. An in vivo massively parallel platform for deciphering tissue-specific regulatory function. bioRxiv doi: 10.1101/2022.11.23.517755

2021

• He J, Kleyman M, Chen J, Alikaya A, Rothenhoefer KM, Ozturk BE, Wirthlin M, Bostan AC, Fish K, Byrne LC, Pfenning AR, Stauffer WR. Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum. (2021) Curr Biol. PMID: 34727523
• Öztürk BE, Johnson ME, Kleyman M, Turunç S, He J, Jabalameli S, Xi Z, Visel M, Dufour VL, Iwabe S, Pompeo Marinho LFL, Aguirre GD, Sahel JA, Schaffer DV, Pfenning AR, Flannery JG, Beltran WA, Stauffer WR, Byrne LC. scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution. (2021) Elife. PMID: 34664552
• Spix TA, Nanivadekar S, Toong N, Kaplow IM, Isett BR, Goksen Y, Pfenning AR, Gittis AH. Population-specific neuromodulation prolongs therapeutic benefits of deep brain stimulation. (2021) Science. PMID: 34618556
• Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology. (2021) J Neurosci. PMID: 34462306
• Seney ML, Kim SM, Glausier JR, Hildebrand MA, Xue X, Zong W, Wang J, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Freyberg Z, Logan RW. Transcriptional Alterations in Dorsolateral Prefrontal Cortex and Nucleus Accumbens Implicate Neuroinflammation and Synaptic Remodeling in Opioid Use Disorder. (2021) Biol Psychiatry. PMID: 34380600

2020

• Lawler AJ, Brown AR, Bouchard RS, Toong N, Kim Y, Velraj N, Fox G, Kleyman M, Kang B, Gittis AH, Pfenning AR. Cell Type-Specific Oxidative Stress Genomic Signatures in the Globus Pallidus of Dopamine-Depleted Mice. (2020) J Neurosci. PMID: 33188066
• Zoonomia Consortium. A comparative genomics multitool for scientific discovery and conservation. (2020) Nature. PMID: 33177664
• Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. (2020) Proc Natl Acad Sci U S A. PMID: 32826334
• Zhang X, Kaplow IM, Wirthlin M, Park TY, Pfenning AR. HALPER facilitates the identification of regulatory element orthologs across species. (2020) Bioinformatics. PMID: 32407523
• Ramamurthy E, Welch G, Cheng J, Yuan Y, Gunsalus L, Bennett DA, Tsai Li-Huei, Pfenning AR. Cell type-specific histone acetylation profiling of Alzheimer’s Disease subjects and integration with genetics. (2020) Front Mol Neurosci. PMID: 36683855

2019

• Wirthlin M, Chang EF, Knörnschild M, Krubitzer LA, Mello CV, Miller CT, Pfenning AR, Vernes SC, Tchernichovski O, Yartsev MM. A Modular Approach to Vocal Learning: Disentangling the Diversity of a Complex Behavioral Trait. (2019) Neuron. PMID: 31600518.
• Glorioso CA, Pfenning AR, Lee SS, Bennett DA, Sibille EL, Kellis M, Guarente LP. Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s disease. (2019) Life Sci Alliance. PMID: 31133613
• Klein HU, McCabe C, Gjoneska E, Sullivan SE, Kaskow BJ, Tang A, Smith RV, Xu J, Pfenning AR, Bernstein BE, Meissner A, Schneider JA, Mostafavi S, Tsai LH, Young-Pearse TL, Bennett DA, De Jager PL. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains. (2019) Nat Neurosci. PMID: 30559478

2016

• Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, Gray JM. High-throughput functional comparison of promoter and enhancer activities. (2016) Genome Res. PMID: 27311442
• Lyons M, Chen L-F, Deng J, Finn C, Pfenning AR, Sabhlok A, Wilson K, West AE. The transcription factor CaRF limits NMDAR-dependent transcription int he developing brain. (2016) J Neurochem. PMID: 26826701

2015

• Madabhushi R*, Gao F*, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, YamawakaH, Pao P-C, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai L-H. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. (2015) Cell. PMID: 26052046
• Gjoneska E*, Pfenning AR*, Kundaje A, Tsai L-H, Kellis M. Conserved epigenomic signals in mice and human reveal immune basis of Alzheimer’s disease. (2015) Nature. PMID: 25693568
• Kundaje A, Meuleman W, Ernst J, et al. (Author #21/93, equal contribution with first author in integrative analysis) Integrative analysis of 111 reference human epigenomes. (2015) Nature. PMID: 25693563

2014

• Pfenning, AR, Hara E, Whitney O, Rivas M, Roulhac P, Ganapathy G, Hartemink AJ, Jarvis ED. Convergent transcriptional specializations in the brains of humans and song learning birds. (2014) Science. PMID: 25504733
• Whitney O*, Pfenning AR*, Howard JT, Blatti CA, Lie F, Ward JM, Wang R, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region enriched networks of behaviorally regulated genes and the singing genome. (2014) Science. PMID: 25504732
• Zhang G, Li C, Li Q, Li B, et al. (Author #51/105). Comparative Genomics Reveal Insights into Avian Genome Evolution and Adaptation. (2014) Science. PMID: 25504712

2013

• Chen CC, Winkler CM, Pfenning AR, Jarvis ED. Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities. (2013) J Comp Neurol. PMID: 23818174
• Jarvis ED, Yu J, Rivas MV, Horita H, Feenders G, Whitney O, Jarvis SC, Jarvis ER, Kubikova L, Puck AE, Siang-Bakshi C, Martin S, McElroy M, Hara E, Howard J, Pfenning A, Mouritsen H, Chen CC, Wada K. Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. (2013) J Comp Neurol. PMID: 23818122

2011

• Liedtke W, McKinley MJ, Walker LL*, Zhang H*, Pfenning AR*, Drago J, Hochendoner SJ, Hilton DL, Lawrence AJ, Denton DA. Relation of addiction genes to hypothalamic gene changes subserving genesis and gratification of a classic instinct, sodium appetite. (2011) Proc Natl Acad Sci. PMID: 21746918

2010

• Pfenning AR, Kim TK, Spotts JM, Hemberg M, Su D, West AE. Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. (2010) PLoS One. PMID: 20523734
• Pfenning AR. Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference. Review. (2010) The Quarterly Review of Biology. Available online
• Warren WC, Clayton DF, et al. (Author #36/80). The genome of a songbird. (2010) Nature. PMID: 20360741

2007

• Pfenning AR, Schwartz R, Barth AL. A comparative genomics approach to identifying the plasticity transcriptome. (2007) BMC Neurosci. PMID: 17355637

* Equal contribution