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Andreas R. Pfenning, Ph.D. - Publications

Affiliations: 
2012 Computational Biology and Bioinformatics Duke University, Durham, NC 
Area:
Vocal learning
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Ramamurthy E, Agarwal S, Toong N, Sestili H, Kaplow IM, Chen Z, Phan B, Pfenning AR. Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease. Plos Computational Biology. 20: e1012356. PMID 39186798 DOI: 10.1371/journal.pcbi.1012356  0.663
2024 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, ... ... Pfenning AR, ... ... Pfenning AR, et al. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science (New York, N.Y.). eabn3263. PMID 38422184 DOI: 10.1126/science.abn3263  0.783
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, ... ... Pfenning AR, et al. Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder. Nature Communications. 15: 878. PMID 38296993 DOI: 10.1038/s41467-024-45165-7  0.741
2023 Chen HY, Phan BN, Shim G, Hamersky GR, Sadowski N, O'Donnell TS, Sripathy SR, Bohlen JF, Pfenning AR, Maher BJ. Psychiatric risk gene Transcription Factor 4 (TCF4) regulates the density and connectivity of distinct inhibitory interneuron subtypes. Molecular Psychiatry. PMID 37770578 DOI: 10.1038/s41380-023-02248-z  0.742
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, Karlsson EK, Lindblad-Toh K, Meyer WK, ... Pfenning AR, ... ... Pfenning AR, et al. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science (New York, N.Y.). 380: eabm7993. PMID 37104615 DOI: 10.1126/science.abm7993  0.809
2023 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, ... ... Pfenning AR, ... ... Pfenning AR, et al. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.). 380: eabn2937. PMID 37104612 DOI: 10.1126/science.abn2937  0.814
2023 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, ... ... Pfenning AR, ... ... Pfenning AR, et al. Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.). 380: eabn3943. PMID 37104599 DOI: 10.1126/science.abn3943  0.81
2023 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, Wallerman O, ... ... Pfenning AR, et al. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. Biorxiv : the Preprint Server For Biology. PMID 36945512 DOI: 10.1101/2023.03.10.531987  0.779
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. Science Advances. 8: eabo4662. PMID 36170369 DOI: 10.1126/sciadv.abo4662  0.713
2022 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, ... ... Pfenning AR, et al. Machine learning sequence prioritization for cell type-specific enhancer design. Elife. 11. PMID 35576146 DOI: 10.7554/eLife.69571  0.786
2022 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. Bmc Genomics. 23: 291. PMID 35410163 DOI: 10.1186/s12864-022-08450-7  0.611
2022 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. Translational Psychiatry. 12: 123. PMID 35347109 DOI: 10.1038/s41398-022-01894-1  0.72
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. Current Biology : Cb. PMID 34727523 DOI: 10.1016/j.cub.2021.10.015  0.567
2021 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. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 34462306 DOI: 10.1523/JNEUROSCI.2534-20.2021  0.812
2021 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. Biological Psychiatry. PMID 34380600 DOI: 10.1016/j.biopsych.2021.06.007  0.704
2020 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, et al. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proceedings of the National Academy of Sciences of the United States of America. PMID 32826334 DOI: 10.1073/Pnas.2010146117  0.319
2020 Zhang X, Kaplow IM, Wirthlin M, Park TY, Pfenning AR. HALPER facilitates the identification of regulatory element orthologs across species. Bioinformatics (Oxford, England). PMID 32407523 DOI: 10.1093/Bioinformatics/Btaa493  0.66
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. Neuron. 104: 87-99. PMID 31600518 DOI: 10.1016/J.Neuron.2019.09.036  0.667
2019 Glorioso CA, Pfenning AR, Lee SS, Bennett DA, Sibille EL, Kellis M, Guarente LP. Rate of brain aging and are synergistic risk factors for Alzheimer's disease. Life Science Alliance. 2. PMID 31133613 DOI: 10.26508/lsa.201900303  0.437
2019 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, et al. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. Nature Neuroscience. 22: 37-46. PMID 30559478 DOI: 10.1038/S41593-018-0291-1  0.369
2016 Rossello RA, Pfenning A, Howard JT, Hochgeschwender U. Characterization and genetic manipulation of primed stem cells into a functional naïve state with ESRRB. World Journal of Stem Cells. 8: 355-366. PMID 27822342 DOI: 10.4252/Wjsc.V8.I10.355  0.594
2016 Nguyen TA, Jones RD, Snavely A, Pfenning A, Kirchner R, Hemberg M, Gray JM. High-throughput functional comparison of promoter and enhancer activities. Genome Research. PMID 27311442 DOI: 10.1101/Gr.204834.116  0.37
2016 Lyons MR, Chen LF, Deng JV, Finn C, Pfenning AR, Sabhlok A, Wilson KM, West AE. The transcription factor CaRF limits NMDAR-dependent transcription in the developing brain. Journal of Neurochemistry. PMID 26826701 DOI: 10.1111/Jnc.13556  0.353
2015 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, et al. Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell. 161: 1592-605. PMID 26052046 DOI: 10.1016/J.Cell.2015.05.032  0.568
2015 Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature. 518: 365-9. PMID 25693568 DOI: 10.1038/Nature14252  0.755
2015 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, ... ... Pfenning AR, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.608
2014 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, et al. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science (New York, N.Y.). 346: 1256846. PMID 25504733 DOI: 10.1126/Science.1256846  0.772
2014 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. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science (New York, N.Y.). 346: 1256780. PMID 25504732 DOI: 10.1126/Science.1256780  0.794
2014 Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, ... ... Pfenning A, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.). 346: 1311-20. PMID 25504712 DOI: 10.1126/Science.1251385  0.792
2013 Chen CC, Winkler CM, Pfenning AR, Jarvis ED. Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities. The Journal of Comparative Neurology. 521: 3666-701. PMID 23818174 DOI: 10.1002/Cne.23406  0.58
2013 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, et al. Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns. The Journal of Comparative Neurology. 521: 3614-65. PMID 23818122 DOI: 10.1002/Cne.23404  0.734
2011 Liedtke WB, 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 12509-14. PMID 21746918 DOI: 10.1073/Pnas.1109199108  0.358
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. Plos One. 5: e10870. PMID 20523734 DOI: 10.1371/Journal.Pone.0010870  0.414
2010 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, ... ... Pfenning AR, et al. The genome of a songbird. Nature. 464: 757-62. PMID 20360741 DOI: 10.1038/Nature08819  0.808
2007 Pfenning AR, Schwartz R, Barth AL. A comparative genomics approach to identifying the plasticity transcriptome. Bmc Neuroscience. 8: 20. PMID 17355637 DOI: 10.1186/1471-2202-8-20  0.446
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