Publications

Addiction, Epigenomics, & Evolution (2020-present)

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”, Science (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, 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. Science. (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, 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. Science. (2023)
Lawler AJ, Ramamurthy, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin ME, 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”. eLIFE , (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 (2022).
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”. Journal of Neuroscience 9, 1 (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 12, 6 (2021).

Phan BN*, Ray MH, Xue X, Fenster RJ, Kohut RJ, Bergman J, Haber SN, Mccullough KM, Fish MK, Glausier JR, Su Q, Tipton AE, Lewis DA, Freyberg Z, Tseng GC, Ressler KJ, Russek SJ, Alekseyev Y, Seney ML, Pfenning AR, Logan RW, "Single nuclei transcriptomics of human and monkey striatum implicates DNA damage, neuroinflammation, and neurodegeneration signaling in opioid use disorder." biorxiv.org/content/10.1101/2023.05.17.541145v2
Ramamurthy E, Agarwal S, Toong N, Kaplow IM, Phan BN, Pfenning AR, “Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer’s disease”, biorxiv.org/content/10.1101/2022.12.02.518903v1.
Brown AR, Fox GA, Kaplow IM, Lawler AJ, Phan BN, Wirthlin ME, Ramamurthy, May GE, Ziheng Chen Z, Su Q, McManus CJ, Pfenning AR, “An in vivo massively parallel platform for deciphering tissue-specific regulatory function”, biorxiv.org/content/10.1101/2022.11.23.517755v1.
Wirthlin ME, Kaplow IM, Lawler AJ, He J, Phan BN, Brown AR, Stauffer WR, Pfenning AR, “The Regulatory Evolution of the Primate Fine-Motor System”, bioRxiv/10.1101/2020.10.27.356733v1.

Molecular Psychiatry & Transcriptomics (2016-2022)

Ramnauth AF*, Maynard KR*, Kardian AS, Phan BN, Tippani M, Rajpurohit S, Hobbs JW, Page SC, Jaffe AE, Martinowich K, “Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex”. Brain Stimulation 15, 2 (2022).
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutierrez-Millan E, Aguilar- Ordonez I, Jaffe AE, Collado-Torres L, “SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses”. BMC Bioinformatics 22, 1 (2021).
Maynard KR, Tippani M, Takahashi Y, Phan BN, Hyde TM, Jaffe AE, Martinowich K, “dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues”. Nucleic Acid Research 48, 11 (2020).
Phan BN*, Bohlen JF*, Davis BA, Ye Z, Chen HY, Mayfield B, Sripathy SR, Cerceo Page S, Campbell MN, Smith HL, Gallop D, Kim H, Thaxton CL, Simon JM, Burke EE, Shin JH, Kennedy AJ, Sweatt JD, Philpot BD, Jaffe AE, Maher BJ, “A Myelin-Related Transcriptomic Profile Is Shared by Pitt-Hopkins Syndrome Models and Human Autism Spectrum Disorder”. Nat Neuroscience 1, 1-11 (2020).
Burke EE, Chenoweth JG, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Straub RE, Hoeppner DJ, Chen HY, Lescure A, Shibbani K, Hamersky GR, Phan BN, Ulrich WS, Valencia C, Jaishankar A, Price AJ, Rajpurohit A, Semick SA, Bu ̈rli R, Barrow JC, Hiler DJ, Page SC, Martinowich K, Hyde TM, Kleinman JE, Berman KF, Apud JA, Cross AJ, Brandon NJ, Weinberger DR, Maher BJ, McKay DG, Jaffe AE, “Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs”. Nat Comm 11, 462 (2020).
Maynard KR, Hobbs JW, Phan BN, Gupta A, Rajpurohit S, Williams C, Rajpurohit N, Shin JH, Jaffe AE, Martinowich K, “BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior”. eLIFE 7, e33676 (2018).
Page SC, Hamersky GR, Gallo RA, Rannals MD, Calcaterra NE, Campbell MN, Mayfield B, Briley A, Phan BN, Jaffe AE, Maher BJ, “The schizophrenia- and autism-associated gene, transcription factor 4 regulates the columnar distribution of layer 2/3 prefrontal pyramidal neurons in an activity-dependent manner”. Mol Psychiatry 23, 304–315 (2016).
Rannals MD, Hamersky GR, Page SC, Campbell MN, Briley A, Gallo RA, Phan BN, Hyde TM, Kleinman JE, Shin JH, Jaffe AE, Weinberger DR, Maher BJ, “Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1”. Neuron 90, 43-55 (2016).

Clinical Research & Collaborations (2017-present)

Desai DD, Yu SE, Salvatore B, Goldberg Z, Bowers EM, Moore JA, Phan BN, Lee SE. Olfactory and Neurological Outcomes of SARS-CoV-2 From Acute Infection to Recovery. Frontiers in Allergy, October (2022).
Morris J*, Olonisakin T*, Moore J, Phan BN, Parker D, Uribe B, Barel S, Bowers E, Buchheit T, Laidlaw TM, Lee S, “Inhibiting the Type 2 Inflammatory Pathway with Dupilumab is Associated with an Increase in IL-4 and IL-18 Production”. International Forum of Allergy and Rhinology, March, 22 (2022).
Perez JL, Ozpinar A, Kano H, Phan BN, Niranjan A, Lunsford LD, “Salvage Stereotactic Radiosurgery in Breast Cancer Patients with Multiple Brain Metastases”. World Neurosurg 125, e479-e486 (2019).
Chen HC , Polisetty TS, Zhu K, Phan BN, Durr NJ, Tian J, Mahoney NR, “A quantitative analysis of factors influencing lower lid retraction and involutional ectropion”. JPRAS 72, 1 (2018).
Haase EB, Phan BN, Goldberg H, “Molecules and Cells: Team-based and Multi-modal Learning Improves Comprehension and Increases Content Retention”. ASEE Annual Conference & Exposition 78, 19703 (2017).