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A. Pfenning · SciRah

Researcher profile · Semantic Scholar

A. Pfenning

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A. Pfenning — researcher profile on SciRah

h-index: 32
Works: 94
Citations: 14K

Most-cited papers

Integrative analysis of 111 reference human epigenomes
A. Kundaje, W. Meuleman, J. Ernst, M. Bilenky +91 more
2015Nature6,166 citations Open access
Semantic Scholar
Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang, Cai Li, Qi-Ye Li, Bo Li +102 more
2014Science989 citations Open access
Semantic Scholar
The genome of a songbird
W. Warren, D. Clayton, H. Ellegren, A. Arnold +78 more
2010Nature895 citations Open access
Semantic Scholar
Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes
R. Madabhushi, Fan Gao, A. Pfenning, L. Pan +12 more
2015Cell678 citations Open access
Semantic Scholar
Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates
Joana Damas, Graham M. Hughes, K. Keough, C. Painter +15 more
2020Proceedings of the National Academy of Sciences of the United States of America596 citations Open access
Semantic Scholar
Loss of epigenetic information as a cause of mammalian aging
Jae-Hyun Yang, Motoshi Hayano, Patrick T. Griffin, João A. Amorim +60 more
2023Cell583 citations
Semantic Scholar
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease
Elizabeta Gjoneska, A. Pfenning, Hansruedi Mathys, G. Quon +3 more
2015Nature556 citations Open access
Semantic Scholar
Convergent transcriptional specializations in the brains of humans and song-learning birds AVIAN GENOMICS
A. Pfenning, Erina Hara, O. Whitney, M. Rivas +21 more
2014417 citations
Semantic Scholar
A comparative genomics multitool for scientific discovery and conservation
D. Genereux, Aitor Serres, J. Armstrong, Jeremy Johnson +44 more
2020Nature347 citations Open access
Semantic Scholar
Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in the aging and Alzheimer human brain
Hans-Ulrich Klein, C. McCabe, Elizabeta Gjoneska, S. Sullivan +13 more
2018Nature Neuroscience240 citations Open access
Semantic Scholar
Global View of the Functional Molecular Organization of the Avian Cerebrum: Mirror Images and Functional Columns
Erich D. Jarvis, Jing Yu, M. Rivas, H. Horita +15 more
2013The Journal of comparative neurology234 citations Open access
Semantic Scholar
Evolutionary constraint and innovation across hundreds of placental mammals
M. Christmas, Irene M. Kaplow, D. Genereux, Michael X. Dong +72 more
2023Science215 citations Open access
Semantic Scholar
High-throughput functional comparison of promoter and enhancer activities
Thomas A. Nguyen, Richard D. Jones, Andrew R. Snavely, A. Pfenning +3 more
2016Genome Research135 citations Open access
Semantic Scholar
Core and region-enriched networks of behaviorally regulated genes and the singing genome
O. Whitney, A. Pfenning, J. Howard, Charles A. Blatti +10 more
2014Science133 citations Open access
Semantic Scholar
Population-specific neuromodulation prolongs therapeutic benefits of deep brain stimulation
Teresa A Spix, Shruti Nanivadekar, Noelle Toong, Irene M. Kaplow +4 more
2021Science131 citations Open access
Semantic Scholar
Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder
Marianne L. Seney, Sam-Moon Kim, J. Glausier, Mariah A. Hildebrand +11 more
2021Biological Psychiatry123 citations Open access
Semantic Scholar
Leveraging base-pair mammalian constraint to understand genetic variation and human disease
Patrick F. Sullivan, Jennifer R. S. Meadows, Steven Gazal, BaDoi N. Phan +35 more
2023Science107 citations Open access
Semantic Scholar
Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities
Chun-Chun Chen, Candace M. Winkler, A. Pfenning, Erich D. Jarvis
2013The Journal of comparative neurology85 citations Open access
Semantic Scholar
Transcriptional and Anatomical Diversity of Medium Spiny Neurons in the Primate Striatum
Jing He, Michael Kleyman, Jian-Jiao Chen, Aydin Alikaya +8 more
2021Current Biology82 citations Open access
Semantic Scholar
Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration
Gwyneth M. Welch, C. Boix, E. Schmauch, J. Dávila-Velderrain +10 more
2021bioRxiv77 citations Open access
Semantic Scholar
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
Irene M. Kaplow, Alyssa J. Lawler, Daniel E. Schäffer, Chaitanya Srinivasan +12 more
2023Science71 citations Open access
Semantic Scholar
Relation of addiction genes to hypothalamic gene changes subserving genesis and gratification of a classic instinct, sodium appetite
W. Liedtke, M. Mckinley, L. L. Walker, Hao Zhang +6 more
2011Proceedings of the National Academy of Sciences of the United States of America63 citations Open access
Semantic Scholar
A Modular Approach to Vocal Learning: Disentangling the Diversity of a Complex Behavioral Trait
Morgan E. Wirthlin, E. Chang, M. Knörnschild, L. Krubitzer +6 more
2019Neuron57 citations Open access
Semantic Scholar
Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder
BaDoi N. Phan, Madelyn H. Ray, Xiangning Xue, Chen Fu +18 more
2024Nature Communications48 citations Open access
Semantic Scholar
scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution
Bilge E. Öztürk, Molly E Johnson, Michael Kleyman, Serhan Turunç +15 more
2021eLife48 citations Open access
Semantic Scholar
Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals
Jae-Hyun Yang, Patrick T. Griffin, Daniel Vera, John K. Apostolides +21 more
2019bioRxiv38 citations Open access
Semantic Scholar
Convergent transcriptional specializations in the brains of humans and song-learning birds
A. Pfenning, Erina Hara, O. Whitney, M. Rivas +21 more
2014Science37 citations Open access
Semantic Scholar
HALPER facilitates the identification of regulatory element orthologs across species
Xiaoyu Zhang, Irene M. Kaplow, Morgan E. Wirthlin, Tae Yoon Park +1 more
2020Bioinform.35 citations Open access
Semantic Scholar
Loss of epigenetic information as a cause of mammalian aging.
Jae-Hyun Yang, Motoshi Hayano, Patrick T. Griffin, João A. Amorim +60 more
2024Cell34 citations
Semantic Scholar
Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder
Xiangning Xue, Wei Zong, J. Glausier, Sam-Moon Kim +8 more
2021bioRxiv34 citations Open access
Semantic Scholar
Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology
Chaitanya Srinivasan, BaDoi N. Phan, Alyssa J. Lawler, Easwaran Ramamurthy +5 more
2020Journal of Neuroscience33 citations Open access
Semantic Scholar
A comparative genomics approach to identifying the plasticity transcriptome
A. Pfenning, R. Schwartz, Alison L. Barth
2007BMC Neuroscience33 citations Open access
Semantic Scholar
Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways
A. Pfenning, Tae-Kyung Kim, J. M. Spotts, M. Hemberg +2 more
2010PLoS ONE32 citations Open access
Semantic Scholar
The transcription factor CaRF limits NMDAR-dependent transcription in the developing brain
Michelle R. Lyons, Liang-Fu Chen, Jie V. Deng, C. Finn +4 more
2016Journal of Neurochemistry25 citations Open access
Semantic Scholar
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements
Morgan E. Wirthlin, Tobias A. Schmid, J. Elie, Xiao-Meng Zhang +22 more
2024Science22 citations Open access
Semantic Scholar
Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Irene M. Kaplow, Daniel E. Schäffer, Morgan E. Wirthlin, Alyssa J. Lawler +3 more
2022BMC Genomics21 citations Open access
Semantic Scholar
Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s disease
C. Glorioso, A. Pfenning, Sam-Sun Lee, D. Bennett +3 more
2019Life Science Alliance19 citations Open access
Semantic Scholar
Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Irene M. Kaplow, Daniel E. Schäffer, Morgan E. Wirthlin, Alyssa J. Lawler +3 more
2020bioRxiv17 citations Open access
Semantic Scholar
The Vertebrate Genomes Project Phase I: A global reference genome resource
G. Formenti, Dominic E. Absolon, L. Abueg, Francine Ackerman +166 more
2026bioRxiv16 citations Open access
Semantic Scholar
Psychiatric risk gene Transcription Factor 4 (TCF4) regulates the density and connectivity of distinct inhibitory interneuron subtypes
Huei-Ying Chen, BaDoi N. Phan, Gina Shim, Gregory R. Hamersky +6 more
2023Molecular Psychiatry16 citations Open access
Semantic Scholar
Machine learning sequence prioritization for cell type-specific enhancer design
Alyssa J. Lawler, Easwaran Ramamurthy, Ashley R. Brown, Naomi Shin +14 more
2022eLife16 citations Open access
Semantic Scholar
Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition
Cynthia M. Arokiaraj, Michael J. Leone, Michael Kleyman, Alexander Chamessian +21 more
2024Cell Reports13 citations Open access
Semantic Scholar
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements
Morgan E. Wirthlin, Tobias A. Schmid, J. Elie, Xiao-Meng Zhang +13 more
2022bioRxiv13 citations Open access
Semantic Scholar
An in vivo systemic massively parallel platform for deciphering animal tissue-specific regulatory function
Ashley R. Brown, Grant A. Fox, Irene M. Kaplow, Alyssa J. Lawler +10 more
2025Frontiers in Genetics11 citations Open access
Semantic Scholar
Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph
Kejun Huang, Tony Zeng, Soner Koc, Alexandra Pettet +14 more
2024medRxiv10 citations Open access
Semantic Scholar
Machine learning identification of enhancers in the rhesus macaque genome.
Jing He, BaDoi N. Phan, Willa G. Kerkhoff, Aydin Alikaya +17 more
2025Neuron9 citations Open access
Semantic Scholar
AI-designed DNA sequences regulate cell-type-specific gene expression
A. Pfenning
2024Nature9 citations
Semantic Scholar
Spatial, transcriptomic and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition
Cynthia M. Arokiaraj, Michael J. Leone, Michael Kleyman, Alexander Chamessian +20 more
2024bioRxiv8 citations Open access
Semantic Scholar
Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development
Andrew S. Clugston, Andrew J. Bodnar, D. Cerqueira, Y. L. Phua +5 more
2021bioRxiv8 citations Open access
Semantic Scholar
Epigenome-wide study uncovers tau pathology-driven changes of chromatin organization in the aging human brain
Hans-Ulrich Klein, C. McCabe, Elizabeta Gjoneska, S. Sullivan +13 more
2018bioRxiv8 citations Open access
Semantic Scholar

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