BaDoi Phan MD, PhD

Arokiaraj CM, Leone MJ, Kleyman M, Chamessian A, Noh MC, Phan BN, Lopes BC, Corrigan KA, Cherupally VK, Yeramosu D, Franusich ME, Podder R, Lele S, Shiers S, Kang B, Kennedy MM, Chen V, Chen Z, Mathys H, Dum RP, Lewis DA, Qadri Y, Price TJ, Pfenning AR, Seal RP. Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition. Cell Rep. 2024 Nov 26;43(11):114876. doi: 10.1016/j.celrep.2024.114876. Epub 2024 Oct 24. PMID: 39453813.

Ibarra AJ, Lopa SH, Phan BN, Himes K, Butters MA, Beck S, Catov JM. Novel Approach to Identify Severe Maternal Morbidity Clusters: A Latent Class Analysis. Am J Perinatol. 2024 Oct 8. doi: 10.1055/a-2418-9955. Epub ahead of print. PMID: 39379025.

Ibarra AJ, Lopa SH, Phan BN, Himes K, Butters MA, Beck S, Catov JM. Novel Approach to Identify Severe Maternal Morbidity Clusters: A Latent Class Analysis. Am J Perinatol. 2024 Oct 8. doi: 10.1055/a-2418-9955. Epub ahead of print. PMID: 39379025.

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 Comput Biol. 2024 Aug 26;20(8):e1012356. doi: 10.1371/journal.pcbi.1012356. PMID: 39186798; PMCID: PMC11389932.

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, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science. 2024 Mar 29;383(6690):eabn3263. doi: 10.1126/science.abn3263. Epub 2024 Mar 29. PMID: 38422184; PMCID: PMC11313673.

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. Nat Commun. 2024 Jan 31;15(1):878. doi: 10.1038/s41467-024-45165-7. PMID: 38296993; PMCID: PMC10831093.

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. Mol Psychiatry. 2023 Nov;28(11):4679-4692. doi: 10.1038/s41380-023-02248-z. Epub 2023 Sep 28. PMID: 37770578; PMCID: PMC11144438.

Gayden J, Puig S, Srinivasan C, Phan BN, Abdelhady G, Buck SA, Gamble MC, Tejeda HA, Dong Y, Pfenning AR, Logan RW, Freyberg Z. Integrative multi-dimensional characterization of striatal projection neuron heterogeneity in adult brain. bioRxiv [Preprint]. 2023 Oct 21:2023.05.04.539488. doi: 10.1101/2023.05.04.539488. PMID: 37205475; PMCID: PMC10187292.

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 Apr 28;380(6643):eabm7993. doi: 10.1126/science.abm7993. Epub 2023 Apr 28. PMID: 37104615; PMCID: PMC10322212.

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 Apr 28;380(6643):eabn2937. doi: 10.1126/science.abn2937. Epub 2023 Apr 28. PMID: 37104612; PMCID: PMC10259825.

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 Apr 28;380(6643):eabn3943. doi: 10.1126/science.abn3943. Epub 2023 Apr 28. PMID: 37104599; PMCID: PMC10250106.

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, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, 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. bioRxiv [Preprint]. 2023 Mar 10:2023.03.10.531987. doi: 10.1101/2023.03.10.531987. Update in: Science. 2023 Apr 28;380(6643):eabn2937. doi: 10.1126/science.abn2937. PMID: 36945512; PMCID: PMC10028973.

Desai DD, Yu SE, Salvatore B, Goldberg Z, Bowers EMR, Moore JA, Phan B, Lee SE. Olfactory and neurological outcomes of SARS-CoV-2 from acute infection to recovery. Front Allergy. 2022 Oct 26;3:1019274. doi: 10.3389/falgy.2022.1019274. PMID: 36389036; PMCID: PMC9644087.

Morris J, Olonisakin TF, Moore JA, Phan B, Parker DM, Uribe BA, Barel SJ, Bowers EMR, Buchheit KM, Laidlaw TM, Lee SE. Inhibiting the type 2 inflammatory pathway with dupilumab is associated with an increase in interleukin-4 and interleukin-18 production. Int Forum Allergy Rhinol. 2022 Oct;12(10):1313-1316. doi: 10.1002/alr.23003. Epub 2022 Apr 29. PMID: 35394682.

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. Elife. 2022 May 16;11:e69571. doi: 10.7554/eLife.69571. PMID: 35576146; PMCID: PMC9110026.

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. Transl Psychiatry. 2022 Mar 26;12(1):123. doi: 10.1038/s41398-022-01894-1. PMID: 35347109; PMCID: PMC8960783.

Ramnauth AD, 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 Stimul. 2022 Mar-Apr;15(2):427-433. doi: 10.1016/j.brs.2022.02.003. Epub 2022 Feb 17. PMID: 35183789; PMCID: PMC8957536.

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. J Neurosci. 2021 Oct 27;41(43):9008-9030. doi: 10.1523/JNEUROSCI.2534-20.2021. Epub 2021 Aug 30. PMID: 34462306; PMCID: PMC8549541.

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. Biol Psychiatry. 2021 Oct 15;90(8):550-562. doi: 10.1016/j.biopsych.2021.06.007. Epub 2021 Jun 12. PMID: 34380600; PMCID: PMC8463497.

Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. BMC Bioinformatics. 2021 Jul 22;22(1):381. doi: 10.1186/s12859-021-04283-5. Erratum for: BMC Bioinformatics. 2021 May 1;22(1):224. doi: 10.1186/s12859-021-04142-3. PMID: 34294043; PMCID: PMC8299680.

Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. BMC Bioinformatics. 2021 May 1;22(1):224. doi: 10.1186/s12859-021-04142-3. Erratum in: BMC Bioinformatics. 2021 Jul 22;22(1):381. doi: 10.1186/s12859-021-04283-5. PMID: 33932985; PMCID: PMC8088074.

Perez JL, Ozpinar A, Kano H, Phan B, Niranjan A, Lunsford LD. Salvage Stereotactic Radiosurgery in Breast Cancer Patients with Multiple Brain Metastases. World Neurosurg. 2019 May;125:e479-e486. doi: 10.1016/j.wneu.2019.01.108. Epub 2019 Jan 31. PMID: 30710716.