dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues
Maynard, Kristen R, Tippani, Madhavi, Takahashi, Yoichiro, Phan, BaDoi N, Hyde, Thomas M, Jaffe, Andrew E, Martinowich, Keri
Published in Nucleic acids research (19.06.2020)
Published in Nucleic acids research (19.06.2020)
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Transcriptional Alterations in Dorsolateral Prefrontal Cortex and Nucleus Accumbens Implicate Neuroinflammation and Synaptic Remodeling in Opioid Use Disorder
Seney, Marianne L., Kim, Sam-Moon, Glausier, Jill R., Hildebrand, Mariah A., Xue, Xiangning, Zong, Wei, Wang, Jiebiao, Shelton, Micah A., Phan, BaDoi N., Srinivasan, Chaitanya, Pfenning, Andreas R., Tseng, George C., Lewis, David A., Freyberg, Zachary, Logan, Ryan W.
Published in Biological psychiatry (1969) (15.10.2021)
Published in Biological psychiatry (1969) (15.10.2021)
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A myelin-related transcriptomic profile is shared by Pitt–Hopkins syndrome models and human autism spectrum disorder
Phan, BaDoi N., Bohlen, Joseph F., Davis, Brittany A., Ye, Zengyou, Chen, Huei-Ying, Mayfield, Brent, Sripathy, Srinidhi Rao, Cerceo Page, Stephanie, Campbell, Morganne N., Smith, Hannah L., Gallop, Danisha, Kim, Hyojin, Thaxton, Courtney L., Simon, Jeremy M., Burke, Emily E., Shin, Joo Heon, Kennedy, Andrew J., Sweatt, J. David, Philpot, Benjamin D., Jaffe, Andrew E., Maher, Brady J.
Published in Nature neuroscience (01.03.2020)
Published in Nature neuroscience (01.03.2020)
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Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
Burke, Emily E., Chenoweth, Joshua G., Shin, Joo Heon, Collado-Torres, Leonardo, Kim, Suel-Kee, Micali, Nicola, Wang, Yanhong, Colantuoni, Carlo, Straub, Richard E., Hoeppner, Daniel J., Chen, Huei-Ying, Sellers, Alana, Shibbani, Kamel, Hamersky, Gregory R., Diaz Bustamante, Marcelo, Phan, BaDoi N., Ulrich, William S., Valencia, Cristian, Jaishankar, Amritha, Price, Amanda J., Rajpurohit, Anandita, Semick, Stephen A., Bürli, Roland W., Barrow, James C., Hiler, Daniel J., Page, Stephanie C., Martinowich, Keri, Hyde, Thomas M., Kleinman, Joel E., Berman, Karen F., Apud, Jose A., Cross, Alan J., Brandon, Nicholas J., Weinberger, Daniel R., Maher, Brady J., McKay, Ronald D. G., Jaffe, Andrew E.
Published in Nature communications (23.01.2020)
Published in Nature communications (23.01.2020)
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Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1
Rannals, Matthew D., Hamersky, Gregory R., Page, Stephanie Cerceo, Campbell, Morganne N., Briley, Aaron, Gallo, Ryan A., Phan, BaDoi N., Hyde, Thomas M., Kleinman, Joel E., Shin, Joo Heon, Jaffe, Andrew E., Weinberger, Daniel R., Maher, Brady J.
Published in Neuron (Cambridge, Mass.) (06.04.2016)
Published in Neuron (Cambridge, Mass.) (06.04.2016)
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SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Eagles, Nicholas J, Burke, Emily E, Leonard, Jacob, Barry, Brianna K, Stolz, Joshua M, Huuki, Louise, Phan, BaDoi N, Serrato, Violeta Larios, Gutiérrez-Millán, Everardo, Aguilar-Ordoñez, Israel, Jaffe, Andrew E, Collado-Torres, Leonardo
Published in BMC bioinformatics (01.05.2021)
Published in BMC bioinformatics (01.05.2021)
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Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology
Srinivasan, Chaitanya, Phan, BaDoi N., Lawler, Alyssa J., Ramamurthy, Easwaran, Kleyman, Michael, Brown, Ashley R., Kaplow, Irene M., Wirthlin, Morgan E., Pfenning, Andreas R.
Published in The Journal of neuroscience (27.10.2021)
Published in The Journal of neuroscience (27.10.2021)
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Psychiatric risk gene Transcription Factor 4 (TCF4) regulates the density and connectivity of distinct inhibitory interneuron subtypes
Chen, Huei-Ying, Phan, BaDoi N., Shim, Gina, Hamersky, Gregory R., Sadowski, Norah, O’Donnell, Thomas S., Sripathy, Srinidhi Rao, Bohlen, Joseph F., Pfenning, Andreas R., Maher, Brady J.
Published in Molecular psychiatry (01.11.2023)
Published in Molecular psychiatry (01.11.2023)
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Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder
Phan, BaDoi N., Ray, Madelyn H., Xue, Xiangning, Fu, Chen, Fenster, Robert J., Kohut, Stephen J., Bergman, Jack, Haber, Suzanne N., McCullough, Kenneth M., Fish, Madeline K., Glausier, Jill R., Su, Qiao, Tipton, Allison E., Lewis, David A., Freyberg, Zachary, Tseng, George C., Russek, Shelley J., Alekseyev, Yuriy, Ressler, Kerry J., Seney, Marianne L., Pfenning, Andreas R., Logan, Ryan W.
Published in Nature communications (31.01.2024)
Published in Nature communications (31.01.2024)
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Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition
Arokiaraj, Cynthia M., Leone, Michael J., Kleyman, Michael, Chamessian, Alexander, Noh, Myung-Chul, Phan, BaDoi N., Lopes, Bettega C., Corrigan, Kelly A., Cherupally, Vijay Kiran, Yeramosu, Deepika, Franusich, Michael E., Podder, Riya, Lele, Sumitra, Shiers, Stephanie, Kang, Byungsoo, Kennedy, Meaghan M., Chen, Viola, Chen, Ziheng, Mathys, Hansruedi, Dum, Richard P., Lewis, David A., Qadri, Yawar, Price, Theodore J., Pfenning, Andreas R., Seal, Rebecca P.
Published in Cell reports (Cambridge) (01.11.2024)
Published in Cell reports (Cambridge) (01.11.2024)
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BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior
Maynard, Kristen R, Hobbs, John W, Phan, BaDoi N, Gupta, Amolika, Rajpurohit, Sumita, Williams, Courtney, Rajpurohit, Anandita, Shin, Joo Heon, Jaffe, Andrew E, Martinowich, Keri
Published in eLife (07.09.2018)
Published in eLife (07.09.2018)
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Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses
Eagles, Nicholas J, Burke, Emily E, Leonard, Jacob, Barry, Brianna K, Stolz, Joshua M, Huuki, Louise, Phan, BaDoi N, Serrato, Violeta Larios, Gutiérrez-Millán, Everardo, Aguilar-Ordoéez, Israel, Jaffe, Andrew E, Collado-Torres, Leonardo
Published in BMC bioinformatics (22.07.2021)
Published in BMC bioinformatics (22.07.2021)
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Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder
Xue, Xiangning, Zong, Wei, Glausier, Jill R., Kim, Sam-Moon, Shelton, Micah A., Phan, BaDoi N., Srinivasan, Chaitanya, Pfenning, Andreas R., Tseng, George C., Lewis, David A., Seney, Marianne L., Logan, Ryan W.
Published in Translational psychiatry (26.03.2022)
Published in Translational psychiatry (26.03.2022)
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Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex
Ramnauth, Anthony D., Maynard, Kristen R., Kardian, Alisha S., Phan, BaDoi N., Tippani, Madhavi, Rajpurohit, Sumita, Hobbs, John W., Page, Stephanie Cerceo, Jaffe, Andrew E., Martinowich, Keri
Published in Brain stimulation (01.03.2022)
Published in Brain stimulation (01.03.2022)
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Machine learning sequence prioritization for cell type-specific enhancer design
Lawler, Alyssa J, Ramamurthy, Easwaran, Brown, Ashley R, Shin, Naomi, Kim, Yeonju, Toong, Noelle, Kaplow, Irene M, Wirthlin, Morgan, Zhang, Xiaoyu, Phan, BaDoi N, Fox, Grant A, Wade, Kirsten, He, Jing, Ozturk, Bilge Esin, Byrne, Leah C, Stauffer, William R, Fish, Kenneth N, Pfenning, Andreas R
Published in eLife (16.05.2022)
Published in eLife (16.05.2022)
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A quantitative analysis of factors influencing lower lid retraction and involutional ectropion
Chen, Hung-Chang, Polisetty, Teja S., Zhu, Kevin, Phan, BaDoi N., Durr, Nicholas J., Tian, Jing, Mahoney, Nicholas R.
Published in Journal of plastic, reconstructive & aesthetic surgery (01.01.2019)
Published in Journal of plastic, reconstructive & aesthetic surgery (01.01.2019)
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Olfactory and neurological outcomes of SARS-CoV-2 from acute infection to recovery
Desai, Deesha D., Yu, Sophie E., Salvatore, Brock, Goldberg, Zoe, Bowers, Eve M. R., Moore, John A., Phan, BaDoi, Lee, Stella E.
Published in Frontiers in allergy (26.10.2022)
Published in Frontiers in allergy (26.10.2022)
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380. Elevated DNA Damage and Neuroinflammatory Markers in Specific Striatal Cell Types Associated With Opioid Use Disorder Using Single Nuclei RNASEQ of Human Postmortem Brain
Logan, Ryan, Phan, BaDoi, Ray, Madelyn, Seney, Marianne, Glausier, Jill, Lewis, David, Pfenning, Andreas
Published in Biological psychiatry (1969) (01.05.2023)
Published in Biological psychiatry (1969) (01.05.2023)
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Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease
Ramamurthy, Easwaran, Agarwal, Snigdha, Toong, Noelle, Sestili, Heather, Kaplow, Irene M, Chen, Ziheng, Phan, BaDoi, Pfenning, Andreas R
Published in PLoS computational biology (26.08.2024)
Published in PLoS computational biology (26.08.2024)
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